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gmx-2019-1-version-variant-2-avx2-log.txt

MdrunNonIntegratorTests - Stefan Becuwe, 03/05/2019 02:37 PM

 
1
[==========] Running 57 tests from 4 test cases.
2
[----------] Global test environment set-up.
3
[----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
4
[ RUN      ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
5

    
6
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]:
7
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
8
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
9
  scheme was introduced, but the group scheme was still the default. The
10
  default is now the Verlet scheme, so you will observe different behaviour.
11

    
12

    
13
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
14
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
15
  that with the Verlet scheme, nstlist has no effect on the accuracy of
16
  your simulation.
17

    
18
Generated 330891 of the 330891 non-bonded parameter combinations
19
Generating 1-4 interactions: fudge = 0.5
20
Generated 330891 of the 330891 1-4 parameter combinations
21
Excluding 2 bonded neighbours molecule type 'SOL'
22
Removing all charge groups because cutoff-scheme=Verlet
23
Number of degrees of freedom in T-Coupling group System is 27.00
24

    
25
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
26
  You are using a plain Coulomb cut-off, which might produce artifacts.
27
  You might want to consider using PME electrostatics.
28

    
29

    
30
This run will generate roughly 0 Mb of data
31

    
32
There were 3 notes
33
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.1 (double precision)
34
Using 1 MPI process
35
Using 1 OpenMP thread 
36

    
37

    
38
NOTE: Thread affinity was not set.
39

    
40
Steepest Descents:
41
   Tolerance (Fmax)   =  1.00000e+01
42
   Number of steps    =            4
43

    
44
Energy minimization reached the maximum number of steps before the forces
45
reached the requested precision Fmax < 10.
46

    
47
writing lowest energy coordinates.
48

    
49
Steepest Descents did not converge to Fmax < 10 in 5 steps.
50
Potential Energy  = -4.79910464433593e+01
51
Maximum force     =  1.86297359800816e+02 on atom 13
52
Norm of force     =  8.77219867200309e+01
53
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
54
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    1.000         
Reading energy frame      2 time    2.000         
Reading energy frame      3 time    3.000         
Reading energy frame      4 time    4.000         
Last energy frame read 4 time    4.000         [       OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (223 ms)
55
[ RUN      ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
56

    
57
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]:
58
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
59
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
60
  scheme was introduced, but the group scheme was still the default. The
61
  default is now the Verlet scheme, so you will observe different behaviour.
62

    
63

    
64
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
65
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
66
  that with the Verlet scheme, nstlist has no effect on the accuracy of
67
  your simulation.
68

    
69
Generated 330891 of the 330891 non-bonded parameter combinations
70
Generating 1-4 interactions: fudge = 0.5
71
Generated 330891 of the 330891 1-4 parameter combinations
72
Excluding 2 bonded neighbours molecule type 'SOL'
73
Removing all charge groups because cutoff-scheme=Verlet
74
Number of degrees of freedom in T-Coupling group System is 27.00
75

    
76
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
77
  You are using a plain Coulomb cut-off, which might produce artifacts.
78
  You might want to consider using PME electrostatics.
79

    
80

    
81
This run will generate roughly 0 Mb of data
82

    
83
There were 3 notes
84
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.1 (double precision)
85
Using 1 MPI process
86
Using 1 OpenMP thread 
87

    
88

    
89
NOTE: Thread affinity was not set.
90

    
91
Polak-Ribiere Conjugate Gradients:
92
   Tolerance (Fmax)   =  1.00000e+01
93
   Number of steps    =            4
94
   F-max             =  3.02331e+02 on atom 3
95
   F-Norm            =  1.18024e+02
96

    
97

    
98
Energy minimization reached the maximum number of steps before the forces
99
reached the requested precision Fmax < 10.
100

    
101
writing lowest energy coordinates.
102

    
103
Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
104
Potential Energy  = -5.58622539552362e+01
105
Maximum force     =  4.27274823589661e+02 on atom 13
106
Norm of force     =  1.84530029788224e+02
107
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
108
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.000         
Reading energy frame      2 time    4.000         
Last energy frame read 2 time    4.000         [       OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (202 ms)
109
[ RUN      ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
110

    
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NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]:
112
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
113
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
114
  scheme was introduced, but the group scheme was still the default. The
115
  default is now the Verlet scheme, so you will observe different behaviour.
116

    
117

    
118
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
119
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
120
  that with the Verlet scheme, nstlist has no effect on the accuracy of
121
  your simulation.
122

    
123
Generated 20503 of the 20503 non-bonded parameter combinations
124
Generating 1-4 interactions: fudge = 1
125
Generated 17396 of the 20503 1-4 parameter combinations
126
Excluding 3 bonded neighbours molecule type 'Glycine'
127
turning H bonds into constraints...
128
Removing all charge groups because cutoff-scheme=Verlet
129
Number of degrees of freedom in T-Coupling group System is 22.00
130

    
131
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
132
  You are using a plain Coulomb cut-off, which might produce artifacts.
133
  You might want to consider using PME electrostatics.
134

    
135

    
136
This run will generate roughly 0 Mb of data
137

    
138
There were 3 notes
139
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.1 (double precision)
140
Using 1 MPI process
141
Using 1 OpenMP thread 
142

    
143

    
144
NOTE: Thread affinity was not set.
145

    
146
Steepest Descents:
147
   Tolerance (Fmax)   =  1.00000e+01
148
   Number of steps    =            4
149

    
150
Energy minimization reached the maximum number of steps before the forces
151
reached the requested precision Fmax < 10.
152

    
153
writing lowest energy coordinates.
154

    
155
Steepest Descents did not converge to Fmax < 10 in 5 steps.
156
Potential Energy  =  3.19376899489615e+02
157
Maximum force     =  9.99884921027275e+03 on atom 9
158
Norm of force     =  4.61669565061010e+03
159
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
160
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    1.000         
Reading energy frame      2 time    2.000         
Reading energy frame      3 time    3.000         
Reading energy frame      4 time    4.000         
Last energy frame read 4 time    4.000         [       OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (127 ms)
161
[ RUN      ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
162

    
163
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]:
164
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
165
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
166
  scheme was introduced, but the group scheme was still the default. The
167
  default is now the Verlet scheme, so you will observe different behaviour.
168

    
169

    
170
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
171
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
172
  that with the Verlet scheme, nstlist has no effect on the accuracy of
173
  your simulation.
174

    
175
Generated 20503 of the 20503 non-bonded parameter combinations
176
Generating 1-4 interactions: fudge = 1
177
Generated 17396 of the 20503 1-4 parameter combinations
178
Excluding 3 bonded neighbours molecule type 'Glycine'
179
turning H bonds into constraints...
180

    
181
NOTE 3 [file glycine_vacuo.top, line 12]:
182
  For accurate cg with LINCS constraints, lincs-order should be 8 or more.
183

    
184
Removing all charge groups because cutoff-scheme=Verlet
185
Number of degrees of freedom in T-Coupling group System is 22.00
186

    
187
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
188
  You are using a plain Coulomb cut-off, which might produce artifacts.
189
  You might want to consider using PME electrostatics.
190

    
191

    
192
This run will generate roughly 0 Mb of data
193

    
194
There were 4 notes
195
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.1 (double precision)
196
Using 1 MPI process
197
Using 1 OpenMP thread 
198

    
199

    
200
NOTE: Thread affinity was not set.
201

    
202
Polak-Ribiere Conjugate Gradients:
203
   Tolerance (Fmax)   =  1.00000e+01
204
   Number of steps    =            4
205
   F-max             =  2.41575e+04 on atom 10
206
   F-Norm            =  1.18451e+04
207

    
208

    
209
Energy minimization reached the maximum number of steps before the forces
210
reached the requested precision Fmax < 10.
211

    
212
writing lowest energy coordinates.
213

    
214
Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
215
Potential Energy  =  1.51743017875794e+02
216
Maximum force     =  7.42089573427939e+03 on atom 9
217
Norm of force     =  3.56929298621805e+03
218
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
219
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.000         
Reading energy frame      2 time    4.000         
Last energy frame read 2 time    4.000         [       OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (116 ms)
220
[ RUN      ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
221

    
222
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]:
223
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
224
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
225
  scheme was introduced, but the group scheme was still the default. The
226
  default is now the Verlet scheme, so you will observe different behaviour.
227

    
228

    
229
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
230
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
231
  that with the Verlet scheme, nstlist has no effect on the accuracy of
232
  your simulation.
233

    
234
Generated 2145 of the 2145 non-bonded parameter combinations
235
Generating 1-4 interactions: fudge = 0.5
236
Generated 2145 of the 2145 1-4 parameter combinations
237
Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
238
turning all bonds into constraints...
239

    
240
NOTE 3 [file unknown]:
241
  You are using constraints on all bonds, whereas the forcefield has been
242
  parametrized only with constraints involving hydrogen atoms. We suggest
243
  using constraints = h-bonds instead, this will also improve performance.
244

    
245
Cleaning up constraints and constant bonded interactions with virtual sites
246
Removed     18           Angles with virtual sites,    21 left
247
Removed     10     Proper Dih.s with virtual sites,    44 left
248
Converted   15      Constraints with virtual sites to connections,     7 left
249
Removing all charge groups because cutoff-scheme=Verlet
250
Number of degrees of freedom in T-Coupling group System is 23.00
251

    
252
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
253
  You are using a plain Coulomb cut-off, which might produce artifacts.
254
  You might want to consider using PME electrostatics.
255

    
256

    
257
This run will generate roughly 0 Mb of data
258

    
259
There were 4 notes
260
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.1 (double precision)
261
Using 1 MPI process
262
Using 1 OpenMP thread 
263

    
264

    
265
NOTE: Thread affinity was not set.
266

    
267
Steepest Descents:
268
   Tolerance (Fmax)   =  1.00000e+01
269
   Number of steps    =            4
270

    
271
Energy minimization reached the maximum number of steps before the forces
272
reached the requested precision Fmax < 10.
273

    
274
writing lowest energy coordinates.
275

    
276
Steepest Descents did not converge to Fmax < 10 in 5 steps.
277
Potential Energy  = -1.56984194095140e+02
278
Maximum force     =  4.56923625858680e+02 on atom 17
279
Norm of force     =  1.83258377483257e+02
280
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
281
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    1.000         
Reading energy frame      2 time    3.000         
Last energy frame read 2 time    3.000         [       OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (64 ms)
282
[ RUN      ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
283

    
284
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]:
285
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
286
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
287
  scheme was introduced, but the group scheme was still the default. The
288
  default is now the Verlet scheme, so you will observe different behaviour.
289

    
290

    
291
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
292
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
293
  that with the Verlet scheme, nstlist has no effect on the accuracy of
294
  your simulation.
295

    
296
Generated 2145 of the 2145 non-bonded parameter combinations
297
Generating 1-4 interactions: fudge = 0.5
298
Generated 2145 of the 2145 1-4 parameter combinations
299
Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
300
turning all bonds into constraints...
301

    
302
NOTE 3 [file unknown]:
303
  You are using constraints on all bonds, whereas the forcefield has been
304
  parametrized only with constraints involving hydrogen atoms. We suggest
305
  using constraints = h-bonds instead, this will also improve performance.
306

    
307

    
308
NOTE 4 [file unknown]:
309
  For accurate cg with LINCS constraints, lincs-order should be 8 or more.
310

    
311
Cleaning up constraints and constant bonded interactions with virtual sites
312
Removed     18           Angles with virtual sites,    21 left
313
Removed     10     Proper Dih.s with virtual sites,    44 left
314
Converted   15      Constraints with virtual sites to connections,     7 left
315
Removing all charge groups because cutoff-scheme=Verlet
316
Number of degrees of freedom in T-Coupling group System is 23.00
317

    
318
NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
319
  You are using a plain Coulomb cut-off, which might produce artifacts.
320
  You might want to consider using PME electrostatics.
321

    
322

    
323
This run will generate roughly 0 Mb of data
324

    
325
There were 5 notes
326
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.1 (double precision)
327
Using 1 MPI process
328
Using 1 OpenMP thread 
329

    
330

    
331
NOTE: Thread affinity was not set.
332

    
333
Polak-Ribiere Conjugate Gradients:
334
   Tolerance (Fmax)   =  1.00000e+01
335
   Number of steps    =            4
336
   F-max             =  1.06800e+03 on atom 28
337
   F-Norm            =  4.26922e+02
338

    
339

    
340
Energy minimization reached the maximum number of steps before the forces
341
reached the requested precision Fmax < 10.
342

    
343
writing lowest energy coordinates.
344

    
345
Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
346
Potential Energy  = -1.69410778941235e+02
347
Maximum force     =  2.18225948179602e+02 on atom 17
348
Norm of force     =  7.92068036008141e+01
349
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
350
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.000         
Reading energy frame      2 time    4.000         
Last energy frame read 2 time    4.000         [       OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (68 ms)
351
[----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (800 ms total)
352

    
353
[----------] 6 tests from MinimizersWork/EnergyMinimizationTest
354
[ RUN      ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
355

    
356
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]:
357
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
358
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
359
  scheme was introduced, but the group scheme was still the default. The
360
  default is now the Verlet scheme, so you will observe different behaviour.
361

    
362

    
363
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
364
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
365
  that with the Verlet scheme, nstlist has no effect on the accuracy of
366
  your simulation.
367

    
368
Generated 1 of the 1 non-bonded parameter combinations
369
Excluding 1 bonded neighbours molecule type 'Argon'
370
Removing all charge groups because cutoff-scheme=Verlet
371
Number of degrees of freedom in T-Coupling group System is 33.00
372
This run will generate roughly 0 Mb of data
373

    
374
There were 2 notes
375
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.1 (double precision)
376
Using 1 MPI process
377
Using 1 OpenMP thread 
378

    
379

    
380
NOTE: Thread affinity was not set.
381

    
382
Steepest Descents:
383
   Tolerance (Fmax)   =  1.00000e+01
384
   Number of steps    =            4
385

    
386
writing lowest energy coordinates.
387

    
388
Steepest Descents converged to Fmax < 10 in 1 steps
389
Potential Energy  = -9.74257075835447e-01
390
Maximum force     =  4.01322929015132e+00 on atom 1
391
Norm of force     =  1.63839399694378e+00
392
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
393
Reading energy frame      0 time    0.000         
Last energy frame read 0 time    0.000         [       OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (60 ms)
394
[ RUN      ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
395

    
396
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]:
397
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
398
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
399
  scheme was introduced, but the group scheme was still the default. The
400
  default is now the Verlet scheme, so you will observe different behaviour.
401

    
402

    
403
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
404
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
405
  that with the Verlet scheme, nstlist has no effect on the accuracy of
406
  your simulation.
407

    
408
Generated 1 of the 1 non-bonded parameter combinations
409
Excluding 1 bonded neighbours molecule type 'Argon'
410
Removing all charge groups because cutoff-scheme=Verlet
411
Number of degrees of freedom in T-Coupling group System is 33.00
412
This run will generate roughly 0 Mb of data
413

    
414
There were 2 notes
415
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.1 (double precision)
416
Using 1 MPI process
417
Using 1 OpenMP thread 
418

    
419

    
420
NOTE: Thread affinity was not set.
421

    
422
Polak-Ribiere Conjugate Gradients:
423
   Tolerance (Fmax)   =  1.00000e+01
424
   Number of steps    =            4
425
   F-max             =  4.01323e+00 on atom 1
426
   F-Norm            =  1.63839e+00
427

    
428

    
429
writing lowest energy coordinates.
430

    
431
Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
432
Potential Energy  = -9.90642313893957e-01
433
Maximum force     =  2.57812909491105e+00 on atom 1
434
Norm of force     =  1.05251679559258e+00
435
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
436
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.000         
Last energy frame read 1 time    0.000         [       OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (56 ms)
437
[ RUN      ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
438

    
439
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]:
440
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
441
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
442
  scheme was introduced, but the group scheme was still the default. The
443
  default is now the Verlet scheme, so you will observe different behaviour.
444

    
445

    
446
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
447
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
448
  that with the Verlet scheme, nstlist has no effect on the accuracy of
449
  your simulation.
450

    
451

    
452
WARNING 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
453
  For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
454

    
455
Generated 1 of the 1 non-bonded parameter combinations
456
Excluding 1 bonded neighbours molecule type 'Argon'
457
Removing all charge groups because cutoff-scheme=Verlet
458
Number of degrees of freedom in T-Coupling group System is 33.00
459
This run will generate roughly 0 Mb of data
460

    
461
There were 2 notes
462

    
463
There was 1 warning
464
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.1 (double precision)
465
Using 1 MPI process
466
Using 1 OpenMP thread 
467

    
468

    
469
NOTE: Thread affinity was not set.
470

    
471
Low-Memory BFGS Minimizer:
472
   Tolerance (Fmax)   =  1.00000e+01
473
   Number of steps    =            4
474
Using 10 BFGS correction steps.
475

    
476
   F-max             =  4.01323e+00 on atom 1
477
   F-Norm            =  1.63839e+00
478

    
479

    
480
writing lowest energy coordinates.
481

    
482
Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps
483
Potential Energy  = -9.90642313893957e-01
484
Maximum force     =  2.57812909491105e+00 on atom 1
485
Norm of force     =  1.05251679559258e+00
486
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
487
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.000         
Last energy frame read 1 time    0.000         [       OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (60 ms)
488
[ RUN      ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
489

    
490
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]:
491
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
492
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
493
  scheme was introduced, but the group scheme was still the default. The
494
  default is now the Verlet scheme, so you will observe different behaviour.
495

    
496

    
497
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
498
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
499
  that with the Verlet scheme, nstlist has no effect on the accuracy of
500
  your simulation.
501

    
502
Generated 20503 of the 20503 non-bonded parameter combinations
503
Generating 1-4 interactions: fudge = 1
504
Generated 17396 of the 20503 1-4 parameter combinations
505
Excluding 3 bonded neighbours molecule type 'Glycine'
506
Removing all charge groups because cutoff-scheme=Verlet
507
Number of degrees of freedom in T-Coupling group System is 27.00
508

    
509
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
510
  You are using a plain Coulomb cut-off, which might produce artifacts.
511
  You might want to consider using PME electrostatics.
512

    
513

    
514
This run will generate roughly 0 Mb of data
515

    
516
There were 3 notes
517
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.1 (double precision)
518
Using 1 MPI process
519
Using 1 OpenMP thread 
520

    
521

    
522
NOTE: Thread affinity was not set.
523

    
524
Steepest Descents:
525
   Tolerance (Fmax)   =  1.00000e+01
526
   Number of steps    =            4
527

    
528
Energy minimization reached the maximum number of steps before the forces
529
reached the requested precision Fmax < 10.
530

    
531
writing lowest energy coordinates.
532

    
533
Steepest Descents did not converge to Fmax < 10 in 5 steps.
534
Potential Energy  =  3.19395484629892e+02
535
Maximum force     =  9.97041707215794e+03 on atom 9
536
Norm of force     =  4.62274878672163e+03
537
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
538
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    1.000         
Reading energy frame      2 time    2.000         
Reading energy frame      3 time    3.000         
Reading energy frame      4 time    4.000         
Last energy frame read 4 time    4.000         [       OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (132 ms)
539
[ RUN      ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
540

    
541
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]:
542
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
543
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
544
  scheme was introduced, but the group scheme was still the default. The
545
  default is now the Verlet scheme, so you will observe different behaviour.
546

    
547

    
548
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
549
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
550
  that with the Verlet scheme, nstlist has no effect on the accuracy of
551
  your simulation.
552

    
553
Generated 20503 of the 20503 non-bonded parameter combinations
554
Generating 1-4 interactions: fudge = 1
555
Generated 17396 of the 20503 1-4 parameter combinations
556
Excluding 3 bonded neighbours molecule type 'Glycine'
557
Removing all charge groups because cutoff-scheme=Verlet
558
Number of degrees of freedom in T-Coupling group System is 27.00
559

    
560
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
561
  You are using a plain Coulomb cut-off, which might produce artifacts.
562
  You might want to consider using PME electrostatics.
563

    
564

    
565
This run will generate roughly 0 Mb of data
566

    
567
There were 3 notes
568
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.1 (double precision)
569
Using 1 MPI process
570
Using 1 OpenMP thread 
571

    
572

    
573
NOTE: Thread affinity was not set.
574

    
575
Polak-Ribiere Conjugate Gradients:
576
   Tolerance (Fmax)   =  1.00000e+01
577
   Number of steps    =            4
578
   F-max             =  2.41672e+04 on atom 10
579
   F-Norm            =  1.19357e+04
580

    
581

    
582
Energy minimization reached the maximum number of steps before the forces
583
reached the requested precision Fmax < 10.
584

    
585
writing lowest energy coordinates.
586

    
587
Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
588
Potential Energy  =  1.56258793634225e+02
589
Maximum force     =  7.50181017498405e+03 on atom 9
590
Norm of force     =  3.61390332570589e+03
591
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
592
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.000         
Reading energy frame      2 time    4.000         
Last energy frame read 2 time    4.000         [       OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (128 ms)
593
[ RUN      ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
594

    
595
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]:
596
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
597
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
598
  scheme was introduced, but the group scheme was still the default. The
599
  default is now the Verlet scheme, so you will observe different behaviour.
600

    
601

    
602
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
603
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
604
  that with the Verlet scheme, nstlist has no effect on the accuracy of
605
  your simulation.
606

    
607

    
608
WARNING 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
609
  For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
610

    
611
Generated 20503 of the 20503 non-bonded parameter combinations
612
Generating 1-4 interactions: fudge = 1
613
Generated 17396 of the 20503 1-4 parameter combinations
614
Excluding 3 bonded neighbours molecule type 'Glycine'
615
Removing all charge groups because cutoff-scheme=Verlet
616
Number of degrees of freedom in T-Coupling group System is 27.00
617

    
618
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
619
  You are using a plain Coulomb cut-off, which might produce artifacts.
620
  You might want to consider using PME electrostatics.
621

    
622

    
623
This run will generate roughly 0 Mb of data
624

    
625
There were 3 notes
626

    
627
There was 1 warning
628
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.1 (double precision)
629
Using 1 MPI process
630
Using 1 OpenMP thread 
631

    
632

    
633
NOTE: Thread affinity was not set.
634

    
635
Low-Memory BFGS Minimizer:
636
   Tolerance (Fmax)   =  1.00000e+01
637
   Number of steps    =            4
638
Using 10 BFGS correction steps.
639

    
640
   F-max             =  2.41672e+04 on atom 10
641
   F-Norm            =  1.19357e+04
642

    
643

    
644
Energy minimization reached the maximum number of steps before the forces
645
reached the requested precision Fmax < 10.
646

    
647
writing lowest energy coordinates.
648

    
649
Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps.
650
Potential Energy  =  1.84722734378548e+03
651
Maximum force     =  2.12615356182376e+04 on atom 9
652
Norm of force     =  1.01988549359681e+04
653
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
654
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.000         
Reading energy frame      2 time    4.000         /dev/shm/gromacs-2019.1/src/testutils/refdata.cpp:922: Failure
655
   In item: /glycine_no_constraints_vacuo/l-bfgs/Potential/Time 4.000000 Step 4 in frame 2
656
    Actual: 1847.2273437854799
657
 Reference: 1847.227343785434
658
Difference: 4.59295e-11 (202 double-prec. ULPs, rel. 2.49e-14)
659
 Tolerance: abs. 4.44089e-11, 100 ULPs
660
Google Test trace:
661
/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/energycomparison.cpp:126: Comparing Potential in Time 4.000000 Step 4 in frame 2
662
/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/minimize.cpp:121: Comparing 'l-bfgs' energy minimization for simulation 'glycine_no_constraints_vacuo'
663
Last energy frame read 2 time    4.000         [  FAILED  ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5, where GetParam() = ("glycine_no_constraints_vacuo", "l-bfgs") (124 ms)
664
[----------] 6 tests from MinimizersWork/EnergyMinimizationTest (560 ms total)
665

    
666
[----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest
667
[ RUN      ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0
668

    
669
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp, line 28]:
670
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
671
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
672
  scheme was introduced, but the group scheme was still the default. The
673
  default is now the Verlet scheme, so you will observe different behaviour.
674

    
675

    
676
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
677
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
678
  that with the Verlet scheme, nstlist has no effect on the accuracy of
679
  your simulation.
680

    
681

    
682
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
683
  Setting nstcalcenergy (100) equal to nstenergy (4)
684

    
685
Generated 1 of the 1 non-bonded parameter combinations
686
Excluding 1 bonded neighbours molecule type 'Argon'
687
Removing all charge groups because cutoff-scheme=Verlet
688
Number of degrees of freedom in T-Coupling group System is 33.00
689

    
690
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
691
  NVE simulation: will use the initial temperature of 68.810 K for
692
  determining the Verlet buffer size
693

    
694
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
695
Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
696
Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
697
Note that mdrun will redetermine rlist based on the actual pair-list setup
698
This run will generate roughly 0 Mb of data
699

    
700
There were 4 notes
701
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0.tpr, VERSION 2019.1 (double precision)
702
Can not increase nstlist because an NVE ensemble is used
703
Using 1 MPI process
704
Using 1 OpenMP thread 
705

    
706

    
707
NOTE: Thread affinity was not set.
708
starting mdrun 'Argon'
709
16 steps,      0.0 ps.
710

    
711
Writing final coordinates.
712

    
713
               Core t (s)   Wall t (s)        (%)
714
       Time:        0.004        0.004       98.6
715
                 (ns/day)    (hour/ns)
716
Performance:      362.217        0.066
717
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0.tpr, VERSION 2019.1 (double precision)
718
Can not increase nstlist because an NVE ensemble is used
719
Using 1 MPI process
720
Using 1 OpenMP thread 
721

    
722

    
723
NOTE: Thread affinity was not set.
724
starting md rerun 'Argon', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_normal.trr'
725

    
726
trr version: GMX_trn_file (double precision)
727
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
728

    
729
NOTE: 11 % of the run time was spent in pair search,
730
      you might want to increase nstlist (this has no effect on accuracy)
731

    
732
               Core t (s)   Wall t (s)        (%)
733
       Time:        0.001        0.001       94.0
734
                 (ns/day)    (hour/ns)
735
Performance:     2524.833        0.010
736
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_normal.edr as double precision energy file
737
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_rerun.edr as double precision energy file
738
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
739

    
740
[       OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (111 ms)
741
[ RUN      ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1
742

    
743
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp, line 28]:
744
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
745
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
746
  scheme was introduced, but the group scheme was still the default. The
747
  default is now the Verlet scheme, so you will observe different behaviour.
748

    
749

    
750
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
751
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
752
  that with the Verlet scheme, nstlist has no effect on the accuracy of
753
  your simulation.
754

    
755

    
756
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
757
  Setting nstcalcenergy (100) equal to nstenergy (4)
758

    
759
Generated 1 of the 1 non-bonded parameter combinations
760
Excluding 1 bonded neighbours molecule type 'Argon'
761
Removing all charge groups because cutoff-scheme=Verlet
762
Number of degrees of freedom in T-Coupling group System is 33.00
763

    
764
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
765
  NVE simulation: will use the initial temperature of 68.810 K for
766
  determining the Verlet buffer size
767

    
768
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
769
Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
770
Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
771
Note that mdrun will redetermine rlist based on the actual pair-list setup
772
This run will generate roughly 0 Mb of data
773

    
774
There were 4 notes
775
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1.tpr, VERSION 2019.1 (double precision)
776
Can not increase nstlist because an NVE ensemble is used
777
Using 1 MPI process
778
Using 1 OpenMP thread 
779

    
780

    
781
NOTE: Thread affinity was not set.
782
starting mdrun 'Argon'
783
16 steps,      0.0 ps.
784

    
785
Writing final coordinates.
786

    
787
               Core t (s)   Wall t (s)        (%)
788
       Time:        0.002        0.002       97.9
789
                 (ns/day)    (hour/ns)
790
Performance:      694.778        0.035
791
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1.tpr, VERSION 2019.1 (double precision)
792
Can not increase nstlist because an NVE ensemble is used
793
Using 1 MPI process
794
Using 1 OpenMP thread 
795

    
796

    
797
NOTE: Thread affinity was not set.
798
starting md rerun 'Argon', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_normal.trr'
799

    
800
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
801

    
802
               Core t (s)   Wall t (s)        (%)
803
       Time:        0.001        0.001       94.8
804
                 (ns/day)    (hour/ns)
805
Performance:     1955.744        0.012
806
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_normal.edr as double precision energy file
807
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_rerun.edr as double precision energy file
808
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
809

    
810
[       OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (113 ms)
811
[ RUN      ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2
812

    
813
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp, line 28]:
814
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
815
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
816
  scheme was introduced, but the group scheme was still the default. The
817
  default is now the Verlet scheme, so you will observe different behaviour.
818

    
819

    
820
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
821
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
822
  that with the Verlet scheme, nstlist has no effect on the accuracy of
823
  your simulation.
824

    
825

    
826
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
827
  Setting nstcalcenergy (100) equal to nstenergy (4)
828

    
829
Generated 1 of the 1 non-bonded parameter combinations
830
Excluding 1 bonded neighbours molecule type 'Argon'
831
Removing all charge groups because cutoff-scheme=Verlet
832
Number of degrees of freedom in T-Coupling group System is 33.00
833
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
834
Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
835
Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
836
Note that mdrun will redetermine rlist based on the actual pair-list setup
837
This run will generate roughly 0 Mb of data
838

    
839
There were 3 notes
840
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2.tpr, VERSION 2019.1 (double precision)
841
Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
842

    
843
Using 1 MPI process
844
Using 1 OpenMP thread 
845

    
846

    
847
NOTE: Thread affinity was not set.
848
starting mdrun 'Argon'
849
16 steps,      0.0 ps.
850

    
851
Writing final coordinates.
852

    
853
               Core t (s)   Wall t (s)        (%)
854
       Time:        0.002        0.002       97.8
855
                 (ns/day)    (hour/ns)
856
Performance:      629.853        0.038
857
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2.tpr, VERSION 2019.1 (double precision)
858
Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
859

    
860
Using 1 MPI process
861
Using 1 OpenMP thread 
862

    
863

    
864
NOTE: Thread affinity was not set.
865
starting md rerun 'Argon', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_normal.trr'
866

    
867
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
868

    
869
NOTE: 11 % of the run time was spent in pair search,
870
      you might want to increase nstlist (this has no effect on accuracy)
871

    
872
               Core t (s)   Wall t (s)        (%)
873
       Time:        0.001        0.001       93.7
874
                 (ns/day)    (hour/ns)
875
Performance:     2330.028        0.010
876
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_normal.edr as double precision energy file
877
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_rerun.edr as double precision energy file
878
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
879

    
880
[       OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (115 ms)
881
[ RUN      ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3
882

    
883
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp, line 28]:
884
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
885
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
886
  scheme was introduced, but the group scheme was still the default. The
887
  default is now the Verlet scheme, so you will observe different behaviour.
888

    
889

    
890
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
891
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
892
  that with the Verlet scheme, nstlist has no effect on the accuracy of
893
  your simulation.
894

    
895

    
896
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
897
  Setting nstcalcenergy (100) equal to nstenergy (4)
898

    
899
Generated 1 of the 1 non-bonded parameter combinations
900
Excluding 1 bonded neighbours molecule type 'Argon'
901
Removing all charge groups because cutoff-scheme=Verlet
902
Number of degrees of freedom in T-Coupling group System is 33.00
903
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
904
Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
905
Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
906
Note that mdrun will redetermine rlist based on the actual pair-list setup
907
This run will generate roughly 0 Mb of data
908

    
909
There were 3 notes
910
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3.tpr, VERSION 2019.1 (double precision)
911
Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
912

    
913
Using 1 MPI process
914
Using 1 OpenMP thread 
915

    
916

    
917
NOTE: Thread affinity was not set.
918
starting mdrun 'Argon'
919
16 steps,      0.0 ps.
920

    
921
Writing final coordinates.
922

    
923
               Core t (s)   Wall t (s)        (%)
924
       Time:        0.003        0.003       98.3
925
                 (ns/day)    (hour/ns)
926
Performance:      497.585        0.048
927
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3.tpr, VERSION 2019.1 (double precision)
928
Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
929

    
930
Using 1 MPI process
931
Using 1 OpenMP thread 
932

    
933

    
934
NOTE: Thread affinity was not set.
935
starting md rerun 'Argon', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_normal.trr'
936

    
937
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
938

    
939
NOTE: 13 % of the run time was spent in pair search,
940
      you might want to increase nstlist (this has no effect on accuracy)
941

    
942
               Core t (s)   Wall t (s)        (%)
943
       Time:        0.001        0.001       93.9
944
                 (ns/day)    (hour/ns)
945
Performance:     2267.425        0.011
946
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_normal.edr as double precision energy file
947
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_rerun.edr as double precision energy file
948
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
949

    
950
[       OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (115 ms)
951
[ RUN      ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4
952

    
953
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp, line 28]:
954
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
955
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
956
  scheme was introduced, but the group scheme was still the default. The
957
  default is now the Verlet scheme, so you will observe different behaviour.
958

    
959

    
960
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
961
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
962
  that with the Verlet scheme, nstlist has no effect on the accuracy of
963
  your simulation.
964

    
965

    
966
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
967
  Setting nstcalcenergy (100) equal to nstenergy (4)
968

    
969
Generated 330891 of the 330891 non-bonded parameter combinations
970
Generating 1-4 interactions: fudge = 0.5
971
Generated 330891 of the 330891 1-4 parameter combinations
972
Excluding 2 bonded neighbours molecule type 'SOL'
973
Removing all charge groups because cutoff-scheme=Verlet
974
Number of degrees of freedom in T-Coupling group System is 27.00
975

    
976
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
977
  NVE simulation: will use the initial temperature of 398.997 K for
978
  determining the Verlet buffer size
979

    
980
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
981
Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
982
Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
983
Note that mdrun will redetermine rlist based on the actual pair-list setup
984

    
985
NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
986
  You are using a plain Coulomb cut-off, which might produce artifacts.
987
  You might want to consider using PME electrostatics.
988

    
989

    
990
This run will generate roughly 0 Mb of data
991

    
992
There were 5 notes
993
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4.tpr, VERSION 2019.1 (double precision)
994
Can not increase nstlist because an NVE ensemble is used
995
Using 1 MPI process
996
Using 1 OpenMP thread 
997

    
998

    
999
NOTE: Thread affinity was not set.
1000
starting mdrun 'spc2'
1001
16 steps,      0.0 ps.
1002

    
1003
Writing final coordinates.
1004

    
1005
               Core t (s)   Wall t (s)        (%)
1006
       Time:        0.004        0.004       98.4
1007
                 (ns/day)    (hour/ns)
1008
Performance:      399.338        0.060
1009
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4.tpr, VERSION 2019.1 (double precision)
1010
Can not increase nstlist because an NVE ensemble is used
1011
Using 1 MPI process
1012
Using 1 OpenMP thread 
1013

    
1014

    
1015
NOTE: Thread affinity was not set.
1016
starting md rerun 'spc2', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_normal.trr'
1017

    
1018
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
1019

    
1020
NOTE: 14 % of the run time was spent in pair search,
1021
      you might want to increase nstlist (this has no effect on accuracy)
1022

    
1023
               Core t (s)   Wall t (s)        (%)
1024
       Time:        0.001        0.001       94.6
1025
                 (ns/day)    (hour/ns)
1026
Performance:     2064.542        0.012
1027
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_normal.edr as double precision energy file
1028
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_rerun.edr as double precision energy file
1029
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
1030

    
1031
[       OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (281 ms)
1032
[ RUN      ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5
1033

    
1034
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp, line 28]:
1035
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
1036
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
1037
  scheme was introduced, but the group scheme was still the default. The
1038
  default is now the Verlet scheme, so you will observe different behaviour.
1039

    
1040

    
1041
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
1042
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
1043
  that with the Verlet scheme, nstlist has no effect on the accuracy of
1044
  your simulation.
1045

    
1046

    
1047
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
1048
  Setting nstcalcenergy (100) equal to nstenergy (4)
1049

    
1050
Generated 330891 of the 330891 non-bonded parameter combinations
1051
Generating 1-4 interactions: fudge = 0.5
1052
Generated 330891 of the 330891 1-4 parameter combinations
1053
Excluding 2 bonded neighbours molecule type 'SOL'
1054
Removing all charge groups because cutoff-scheme=Verlet
1055
Number of degrees of freedom in T-Coupling group System is 27.00
1056

    
1057
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
1058
  NVE simulation: will use the initial temperature of 398.997 K for
1059
  determining the Verlet buffer size
1060

    
1061
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
1062
Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
1063
Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
1064
Note that mdrun will redetermine rlist based on the actual pair-list setup
1065

    
1066
NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
1067
  You are using a plain Coulomb cut-off, which might produce artifacts.
1068
  You might want to consider using PME electrostatics.
1069

    
1070

    
1071
This run will generate roughly 0 Mb of data
1072

    
1073
There were 5 notes
1074
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5.tpr, VERSION 2019.1 (double precision)
1075
Can not increase nstlist because an NVE ensemble is used
1076
Using 1 MPI process
1077
Using 1 OpenMP thread 
1078

    
1079

    
1080
NOTE: Thread affinity was not set.
1081
starting mdrun 'spc2'
1082
16 steps,      0.0 ps.
1083

    
1084
Writing final coordinates.
1085

    
1086
               Core t (s)   Wall t (s)        (%)
1087
       Time:        0.004        0.004       98.8
1088
                 (ns/day)    (hour/ns)
1089
Performance:      348.233        0.069
1090
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5.tpr, VERSION 2019.1 (double precision)
1091
Can not increase nstlist because an NVE ensemble is used
1092
Using 1 MPI process
1093
Using 1 OpenMP thread 
1094

    
1095

    
1096
NOTE: Thread affinity was not set.
1097
starting md rerun 'spc2', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_normal.trr'
1098

    
1099
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
1100

    
1101
NOTE: 15 % of the run time was spent in pair search,
1102
      you might want to increase nstlist (this has no effect on accuracy)
1103

    
1104
               Core t (s)   Wall t (s)        (%)
1105
       Time:        0.001        0.001       94.1
1106
                 (ns/day)    (hour/ns)
1107
Performance:     2336.213        0.010
1108
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_normal.edr as double precision energy file
1109
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_rerun.edr as double precision energy file
1110
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
1111

    
1112
[       OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (270 ms)
1113
[ RUN      ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6
1114

    
1115
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp, line 28]:
1116
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
1117
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
1118
  scheme was introduced, but the group scheme was still the default. The
1119
  default is now the Verlet scheme, so you will observe different behaviour.
1120

    
1121

    
1122
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
1123
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
1124
  that with the Verlet scheme, nstlist has no effect on the accuracy of
1125
  your simulation.
1126

    
1127

    
1128
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
1129
  Setting nstcalcenergy (100) equal to nstenergy (4)
1130

    
1131
Generated 330891 of the 330891 non-bonded parameter combinations
1132
Generating 1-4 interactions: fudge = 0.5
1133
Generated 330891 of the 330891 1-4 parameter combinations
1134
Excluding 2 bonded neighbours molecule type 'SOL'
1135
Removing all charge groups because cutoff-scheme=Verlet
1136
Number of degrees of freedom in T-Coupling group System is 27.00
1137
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
1138
Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm
1139
Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm
1140
Note that mdrun will redetermine rlist based on the actual pair-list setup
1141

    
1142
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
1143
  You are using a plain Coulomb cut-off, which might produce artifacts.
1144
  You might want to consider using PME electrostatics.
1145

    
1146

    
1147
This run will generate roughly 0 Mb of data
1148

    
1149
There were 4 notes
1150
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6.tpr, VERSION 2019.1 (double precision)
1151
Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
1152

    
1153
Using 1 MPI process
1154
Using 1 OpenMP thread 
1155

    
1156

    
1157
NOTE: Thread affinity was not set.
1158
starting mdrun 'spc2'
1159
16 steps,      0.0 ps.
1160

    
1161
Writing final coordinates.
1162

    
1163
               Core t (s)   Wall t (s)        (%)
1164
       Time:        0.004        0.004       98.3
1165
                 (ns/day)    (hour/ns)
1166
Performance:      399.080        0.060
1167
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6.tpr, VERSION 2019.1 (double precision)
1168
Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
1169

    
1170
Using 1 MPI process
1171
Using 1 OpenMP thread 
1172

    
1173

    
1174
NOTE: Thread affinity was not set.
1175
starting md rerun 'spc2', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_normal.trr'
1176

    
1177
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
1178

    
1179
NOTE: 15 % of the run time was spent in pair search,
1180
      you might want to increase nstlist (this has no effect on accuracy)
1181

    
1182
               Core t (s)   Wall t (s)        (%)
1183
       Time:        0.001        0.001       93.9
1184
                 (ns/day)    (hour/ns)
1185
Performance:     2288.482        0.010
1186
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_normal.edr as double precision energy file
1187
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_rerun.edr as double precision energy file
1188
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
1189

    
1190
[       OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (276 ms)
1191
[ RUN      ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7
1192

    
1193
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp, line 28]:
1194
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
1195
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
1196
  scheme was introduced, but the group scheme was still the default. The
1197
  default is now the Verlet scheme, so you will observe different behaviour.
1198

    
1199

    
1200
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
1201
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
1202
  that with the Verlet scheme, nstlist has no effect on the accuracy of
1203
  your simulation.
1204

    
1205

    
1206
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
1207
  Setting nstcalcenergy (100) equal to nstenergy (4)
1208

    
1209
Generated 330891 of the 330891 non-bonded parameter combinations
1210
Generating 1-4 interactions: fudge = 0.5
1211
Generated 330891 of the 330891 1-4 parameter combinations
1212
Excluding 2 bonded neighbours molecule type 'SOL'
1213
Removing all charge groups because cutoff-scheme=Verlet
1214
Number of degrees of freedom in T-Coupling group System is 27.00
1215
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
1216
Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
1217
Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
1218
Note that mdrun will redetermine rlist based on the actual pair-list setup
1219

    
1220
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
1221
  You are using a plain Coulomb cut-off, which might produce artifacts.
1222
  You might want to consider using PME electrostatics.
1223

    
1224

    
1225
This run will generate roughly 0 Mb of data
1226

    
1227
There were 4 notes
1228
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7.tpr, VERSION 2019.1 (double precision)
1229
Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
1230

    
1231
Using 1 MPI process
1232
Using 1 OpenMP thread 
1233

    
1234

    
1235
NOTE: Thread affinity was not set.
1236
starting mdrun 'spc2'
1237
16 steps,      0.0 ps.
1238

    
1239
Writing final coordinates.
1240

    
1241
               Core t (s)   Wall t (s)        (%)
1242
       Time:        0.003        0.003       97.8
1243
                 (ns/day)    (hour/ns)
1244
Performance:      573.772        0.042
1245
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7.tpr, VERSION 2019.1 (double precision)
1246
Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
1247

    
1248
Using 1 MPI process
1249
Using 1 OpenMP thread 
1250

    
1251

    
1252
NOTE: Thread affinity was not set.
1253
starting md rerun 'spc2', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_normal.trr'
1254

    
1255
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
1256

    
1257
NOTE: 22 % of the run time was spent in pair search,
1258
      you might want to increase nstlist (this has no effect on accuracy)
1259

    
1260
               Core t (s)   Wall t (s)        (%)
1261
       Time:        0.001        0.001       94.8
1262
                 (ns/day)    (hour/ns)
1263
Performance:     1997.598        0.012
1264
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_normal.edr as double precision energy file
1265
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_rerun.edr as double precision energy file
1266
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
1267

    
1268
[       OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (270 ms)
1269
[ RUN      ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8
1270

    
1271
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp, line 28]:
1272
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
1273
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
1274
  scheme was introduced, but the group scheme was still the default. The
1275
  default is now the Verlet scheme, so you will observe different behaviour.
1276

    
1277

    
1278
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
1279
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
1280
  that with the Verlet scheme, nstlist has no effect on the accuracy of
1281
  your simulation.
1282

    
1283

    
1284
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
1285
  Setting nstcalcenergy (100) equal to nstenergy (4)
1286

    
1287
Generated 2145 of the 2145 non-bonded parameter combinations
1288
Generating 1-4 interactions: fudge = 0.5
1289
Generated 2145 of the 2145 1-4 parameter combinations
1290
Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
1291
turning all bonds into constraints...
1292

    
1293
NOTE 4 [file unknown]:
1294
  You are using constraints on all bonds, whereas the forcefield has been
1295
  parametrized only with constraints involving hydrogen atoms. We suggest
1296
  using constraints = h-bonds instead, this will also improve performance.
1297

    
1298
Cleaning up constraints and constant bonded interactions with virtual sites
1299
Removed     18           Angles with virtual sites,    21 left
1300
Removed     10     Proper Dih.s with virtual sites,    44 left
1301
Converted   15      Constraints with virtual sites to connections,     7 left
1302
Removing all charge groups because cutoff-scheme=Verlet
1303
Number of degrees of freedom in T-Coupling group System is 23.00
1304

    
1305
NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
1306
  NVE simulation: will use the initial temperature of 456.887 K for
1307
  determining the Verlet buffer size
1308

    
1309
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
1310

    
1311
NOTE 6 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
1312
  There are 9 non-linear virtual site constructions. Their contribution to
1313
  the energy error is approximated. In most cases this does not affect the
1314
  error significantly.
1315

    
1316
Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
1317
Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
1318
Note that mdrun will redetermine rlist based on the actual pair-list setup
1319

    
1320
NOTE 7 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
1321
  You are using a plain Coulomb cut-off, which might produce artifacts.
1322
  You might want to consider using PME electrostatics.
1323

    
1324

    
1325
This run will generate roughly 0 Mb of data
1326

    
1327
There were 7 notes
1328
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8.tpr, VERSION 2019.1 (double precision)
1329
Can not increase nstlist because an NVE ensemble is used
1330
Using 1 MPI process
1331
Using 1 OpenMP thread 
1332

    
1333

    
1334
NOTE: Thread affinity was not set.
1335
starting mdrun 'Alanine dipeptide in vacuo'
1336
16 steps,      0.0 ps.
1337

    
1338
Writing final coordinates.
1339

    
1340
               Core t (s)   Wall t (s)        (%)
1341
       Time:        0.003        0.004       97.3
1342
                 (ns/day)    (hour/ns)
1343
Performance:      414.771        0.058
1344
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8.tpr, VERSION 2019.1 (double precision)
1345
Can not increase nstlist because an NVE ensemble is used
1346
Using 1 MPI process
1347
Using 1 OpenMP thread 
1348

    
1349

    
1350
NOTE: Thread affinity was not set.
1351
starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_normal.trr'
1352

    
1353
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
1354

    
1355
NOTE: 13 % of the run time was spent in pair search,
1356
      you might want to increase nstlist (this has no effect on accuracy)
1357

    
1358
               Core t (s)   Wall t (s)        (%)
1359
       Time:        0.001        0.001       96.3
1360
                 (ns/day)    (hour/ns)
1361
Performance:     1380.371        0.017
1362
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_normal.edr as double precision energy file
1363
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_rerun.edr as double precision energy file
1364
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
1365

    
1366
[       OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (127 ms)
1367
[ RUN      ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9
1368

    
1369
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp, line 28]:
1370
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
1371
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
1372
  scheme was introduced, but the group scheme was still the default. The
1373
  default is now the Verlet scheme, so you will observe different behaviour.
1374

    
1375

    
1376
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
1377
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
1378
  that with the Verlet scheme, nstlist has no effect on the accuracy of
1379
  your simulation.
1380

    
1381

    
1382
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
1383
  Setting nstcalcenergy (100) equal to nstenergy (4)
1384

    
1385
Generated 2145 of the 2145 non-bonded parameter combinations
1386
Generating 1-4 interactions: fudge = 0.5
1387
Generated 2145 of the 2145 1-4 parameter combinations
1388
Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
1389
turning all bonds into constraints...
1390

    
1391
NOTE 4 [file unknown]:
1392
  You are using constraints on all bonds, whereas the forcefield has been
1393
  parametrized only with constraints involving hydrogen atoms. We suggest
1394
  using constraints = h-bonds instead, this will also improve performance.
1395

    
1396
Cleaning up constraints and constant bonded interactions with virtual sites
1397
Removed     18           Angles with virtual sites,    21 left
1398
Removed     10     Proper Dih.s with virtual sites,    44 left
1399
Converted   15      Constraints with virtual sites to connections,     7 left
1400
Removing all charge groups because cutoff-scheme=Verlet
1401
Number of degrees of freedom in T-Coupling group System is 23.00
1402

    
1403
NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
1404
  NVE simulation: will use the initial temperature of 456.887 K for
1405
  determining the Verlet buffer size
1406

    
1407
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
1408

    
1409
NOTE 6 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
1410
  There are 9 non-linear virtual site constructions. Their contribution to
1411
  the energy error is approximated. In most cases this does not affect the
1412
  error significantly.
1413

    
1414
Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
1415
Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
1416
Note that mdrun will redetermine rlist based on the actual pair-list setup
1417

    
1418
NOTE 7 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
1419
  You are using a plain Coulomb cut-off, which might produce artifacts.
1420
  You might want to consider using PME electrostatics.
1421

    
1422

    
1423
This run will generate roughly 0 Mb of data
1424

    
1425
There were 7 notes
1426
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9.tpr, VERSION 2019.1 (double precision)
1427
Can not increase nstlist because an NVE ensemble is used
1428
Using 1 MPI process
1429
Using 1 OpenMP thread 
1430

    
1431

    
1432
NOTE: Thread affinity was not set.
1433
starting mdrun 'Alanine dipeptide in vacuo'
1434
16 steps,      0.0 ps.
1435

    
1436
Writing final coordinates.
1437

    
1438
               Core t (s)   Wall t (s)        (%)
1439
       Time:        0.005        0.005       98.4
1440
                 (ns/day)    (hour/ns)
1441
Performance:      316.512        0.076
1442
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9.tpr, VERSION 2019.1 (double precision)
1443
Can not increase nstlist because an NVE ensemble is used
1444
Using 1 MPI process
1445
Using 1 OpenMP thread 
1446

    
1447

    
1448
NOTE: Thread affinity was not set.
1449
starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_normal.trr'
1450

    
1451
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
1452

    
1453
NOTE: 16 % of the run time was spent in pair search,
1454
      you might want to increase nstlist (this has no effect on accuracy)
1455

    
1456
               Core t (s)   Wall t (s)        (%)
1457
       Time:        0.001        0.001       96.5
1458
                 (ns/day)    (hour/ns)
1459
Performance:     1468.206        0.016
1460
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_normal.edr as double precision energy file
1461
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_rerun.edr as double precision energy file
1462
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
1463

    
1464
[       OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (133 ms)
1465
[ RUN      ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10
1466

    
1467
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp, line 28]:
1468
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
1469
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
1470
  scheme was introduced, but the group scheme was still the default. The
1471
  default is now the Verlet scheme, so you will observe different behaviour.
1472

    
1473

    
1474
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
1475
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
1476
  that with the Verlet scheme, nstlist has no effect on the accuracy of
1477
  your simulation.
1478

    
1479

    
1480
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
1481
  Setting nstcalcenergy (100) equal to nstenergy (4)
1482

    
1483
Generated 2145 of the 2145 non-bonded parameter combinations
1484
Generating 1-4 interactions: fudge = 0.5
1485
Generated 2145 of the 2145 1-4 parameter combinations
1486
Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
1487
turning all bonds into constraints...
1488

    
1489
NOTE 4 [file unknown]:
1490
  You are using constraints on all bonds, whereas the forcefield has been
1491
  parametrized only with constraints involving hydrogen atoms. We suggest
1492
  using constraints = h-bonds instead, this will also improve performance.
1493

    
1494
Cleaning up constraints and constant bonded interactions with virtual sites
1495
Removed     18           Angles with virtual sites,    21 left
1496
Removed     10     Proper Dih.s with virtual sites,    44 left
1497
Converted   15      Constraints with virtual sites to connections,     7 left
1498
Removing all charge groups because cutoff-scheme=Verlet
1499
Number of degrees of freedom in T-Coupling group System is 23.00
1500
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
1501

    
1502
NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
1503
  There are 9 non-linear virtual site constructions. Their contribution to
1504
  the energy error is approximated. In most cases this does not affect the
1505
  error significantly.
1506

    
1507
Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
1508
Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
1509
Note that mdrun will redetermine rlist based on the actual pair-list setup
1510

    
1511
NOTE 6 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
1512
  You are using a plain Coulomb cut-off, which might produce artifacts.
1513
  You might want to consider using PME electrostatics.
1514

    
1515

    
1516
This run will generate roughly 0 Mb of data
1517

    
1518
There were 6 notes
1519
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10.tpr, VERSION 2019.1 (double precision)
1520
Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
1521

    
1522
Using 1 MPI process
1523
Using 1 OpenMP thread 
1524

    
1525

    
1526
NOTE: Thread affinity was not set.
1527
starting mdrun 'Alanine dipeptide in vacuo'
1528
16 steps,      0.0 ps.
1529

    
1530
Writing final coordinates.
1531

    
1532
               Core t (s)   Wall t (s)        (%)
1533
       Time:        0.004        0.004       98.2
1534
                 (ns/day)    (hour/ns)
1535
Performance:      403.286        0.060
1536
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10.tpr, VERSION 2019.1 (double precision)
1537
Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
1538

    
1539
Using 1 MPI process
1540
Using 1 OpenMP thread 
1541

    
1542

    
1543
NOTE: Thread affinity was not set.
1544
starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_normal.trr'
1545

    
1546
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
1547

    
1548
NOTE: 14 % of the run time was spent in pair search,
1549
      you might want to increase nstlist (this has no effect on accuracy)
1550

    
1551
               Core t (s)   Wall t (s)        (%)
1552
       Time:        0.001        0.001       96.5
1553
                 (ns/day)    (hour/ns)
1554
Performance:     1440.738        0.017
1555
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_normal.edr as double precision energy file
1556
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_rerun.edr as double precision energy file
1557
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
1558

    
1559
[       OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (139 ms)
1560
[ RUN      ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11
1561

    
1562
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp, line 28]:
1563
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
1564
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
1565
  scheme was introduced, but the group scheme was still the default. The
1566
  default is now the Verlet scheme, so you will observe different behaviour.
1567

    
1568

    
1569
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
1570
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
1571
  that with the Verlet scheme, nstlist has no effect on the accuracy of
1572
  your simulation.
1573

    
1574

    
1575
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
1576
  Setting nstcalcenergy (100) equal to nstenergy (4)
1577

    
1578
Generated 2145 of the 2145 non-bonded parameter combinations
1579
Generating 1-4 interactions: fudge = 0.5
1580
Generated 2145 of the 2145 1-4 parameter combinations
1581
Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
1582
turning all bonds into constraints...
1583

    
1584
NOTE 4 [file unknown]:
1585
  You are using constraints on all bonds, whereas the forcefield has been
1586
  parametrized only with constraints involving hydrogen atoms. We suggest
1587
  using constraints = h-bonds instead, this will also improve performance.
1588

    
1589
Cleaning up constraints and constant bonded interactions with virtual sites
1590
Removed     18           Angles with virtual sites,    21 left
1591
Removed     10     Proper Dih.s with virtual sites,    44 left
1592
Converted   15      Constraints with virtual sites to connections,     7 left
1593
Removing all charge groups because cutoff-scheme=Verlet
1594
Number of degrees of freedom in T-Coupling group System is 23.00
1595
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
1596

    
1597
NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
1598
  There are 9 non-linear virtual site constructions. Their contribution to
1599
  the energy error is approximated. In most cases this does not affect the
1600
  error significantly.
1601

    
1602
Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
1603
Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
1604
Note that mdrun will redetermine rlist based on the actual pair-list setup
1605

    
1606
NOTE 6 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
1607
  You are using a plain Coulomb cut-off, which might produce artifacts.
1608
  You might want to consider using PME electrostatics.
1609

    
1610

    
1611
This run will generate roughly 0 Mb of data
1612

    
1613
There were 6 notes
1614
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11.tpr, VERSION 2019.1 (double precision)
1615
Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
1616

    
1617
Using 1 MPI process
1618
Using 1 OpenMP thread 
1619

    
1620

    
1621
NOTE: Thread affinity was not set.
1622
starting mdrun 'Alanine dipeptide in vacuo'
1623
16 steps,      0.0 ps.
1624

    
1625
Writing final coordinates.
1626

    
1627
               Core t (s)   Wall t (s)        (%)
1628
       Time:        0.005        0.005       98.6
1629
                 (ns/day)    (hour/ns)
1630
Performance:      318.262        0.075
1631
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11.tpr, VERSION 2019.1 (double precision)
1632
Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
1633

    
1634
Using 1 MPI process
1635
Using 1 OpenMP thread 
1636

    
1637

    
1638
NOTE: Thread affinity was not set.
1639
starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_normal.trr'
1640

    
1641
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
1642

    
1643
NOTE: 14 % of the run time was spent in pair search,
1644
      you might want to increase nstlist (this has no effect on accuracy)
1645

    
1646
               Core t (s)   Wall t (s)        (%)
1647
       Time:        0.001        0.001       96.7
1648
                 (ns/day)    (hour/ns)
1649
Performance:     1459.510        0.016
1650
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_normal.edr as double precision energy file
1651
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_rerun.edr as double precision energy file
1652
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
1653

    
1654
[       OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (137 ms)
1655
[----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (2088 ms total)
1656

    
1657
[----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest
1658
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0
1659

    
1660
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp, line 42]:
1661
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
1662
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
1663
  scheme was introduced, but the group scheme was still the default. The
1664
  default is now the Verlet scheme, so you will observe different behaviour.
1665

    
1666

    
1667
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
1668
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
1669
  that with the Verlet scheme, nstlist has no effect on the accuracy of
1670
  your simulation.
1671

    
1672

    
1673
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
1674
  Setting nstcalcenergy (100) equal to nstenergy (4)
1675

    
1676
Generated 2485 of the 2485 non-bonded parameter combinations
1677
Generating 1-4 interactions: fudge = 0.5
1678
Generated 2485 of the 2485 1-4 parameter combinations
1679
Excluding 3 bonded neighbours molecule type 'nonanol'
1680
turning H bonds into constraints...
1681
Excluding 2 bonded neighbours molecule type 'SOL'
1682
turning H bonds into constraints...
1683
Removing all charge groups because cutoff-scheme=Verlet
1684
Number of degrees of freedom in T-Coupling group System is 79.00
1685

    
1686
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
1687
  NVE simulation: will use the initial temperature of 293.480 K for
1688
  determining the Verlet buffer size
1689

    
1690
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
1691
Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
1692
Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
1693
Note that mdrun will redetermine rlist based on the actual pair-list setup
1694

    
1695
NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
1696
  You are using a plain Coulomb cut-off, which might produce artifacts.
1697
  You might want to consider using PME electrostatics.
1698

    
1699

    
1700
This run will generate roughly 0 Mb of data
1701

    
1702
There were 5 notes
1703
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0.tpr, VERSION 2019.1 (double precision)
1704
Can not increase nstlist because an NVE ensemble is used
1705
Using 1 MPI process
1706
Using 1 OpenMP thread 
1707

    
1708

    
1709
NOTE: Thread affinity was not set.
1710
starting mdrun '30 system in water'
1711
16 steps,      0.0 ps.
1712

    
1713
Writing final coordinates.
1714

    
1715
               Core t (s)   Wall t (s)        (%)
1716
       Time:        0.004        0.004       98.6
1717
                 (ns/day)    (hour/ns)
1718
Performance:      351.251        0.068
1719
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0.tpr, VERSION 2019.1 (double precision)
1720
Can not increase nstlist because an NVE ensemble is used
1721
Using 1 MPI process
1722
Using 1 OpenMP thread 
1723

    
1724

    
1725
NOTE: Thread affinity was not set.
1726
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_normal.trr'
1727

    
1728
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
1729

    
1730
NOTE: 12 % of the run time was spent in pair search,
1731
      you might want to increase nstlist (this has no effect on accuracy)
1732

    
1733
               Core t (s)   Wall t (s)        (%)
1734
       Time:        0.001        0.001       96.7
1735
                 (ns/day)    (hour/ns)
1736
Performance:     1062.354        0.023
1737
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_normal.edr as double precision energy file
1738
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_rerun.edr as double precision energy file
1739
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
1740

    
1741
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (120 ms)
1742
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1
1743

    
1744
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp, line 42]:
1745
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
1746
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
1747
  scheme was introduced, but the group scheme was still the default. The
1748
  default is now the Verlet scheme, so you will observe different behaviour.
1749

    
1750

    
1751
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
1752
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
1753
  that with the Verlet scheme, nstlist has no effect on the accuracy of
1754
  your simulation.
1755

    
1756

    
1757
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
1758
  Setting nstcalcenergy (100) equal to nstenergy (4)
1759

    
1760
Generated 2485 of the 2485 non-bonded parameter combinations
1761
Generating 1-4 interactions: fudge = 0.5
1762
Generated 2485 of the 2485 1-4 parameter combinations
1763
Excluding 3 bonded neighbours molecule type 'nonanol'
1764
turning H bonds into constraints...
1765
Excluding 2 bonded neighbours molecule type 'SOL'
1766
turning H bonds into constraints...
1767
Removing all charge groups because cutoff-scheme=Verlet
1768
Number of degrees of freedom in T-Coupling group System is 79.00
1769

    
1770
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
1771
  NVE simulation: will use the initial temperature of 293.480 K for
1772
  determining the Verlet buffer size
1773

    
1774
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
1775
Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
1776
Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
1777
Note that mdrun will redetermine rlist based on the actual pair-list setup
1778

    
1779
NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
1780
  You are using a plain Coulomb cut-off, which might produce artifacts.
1781
  You might want to consider using PME electrostatics.
1782

    
1783

    
1784
This run will generate roughly 0 Mb of data
1785

    
1786
There were 5 notes
1787
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1.tpr, VERSION 2019.1 (double precision)
1788
Can not increase nstlist because an NVE ensemble is used
1789
Using 1 MPI process
1790
Using 1 OpenMP thread 
1791

    
1792

    
1793
NOTE: Thread affinity was not set.
1794
starting mdrun '30 system in water'
1795
16 steps,      0.0 ps.
1796

    
1797
Writing final coordinates.
1798

    
1799
               Core t (s)   Wall t (s)        (%)
1800
       Time:        0.005        0.005       98.6
1801
                 (ns/day)    (hour/ns)
1802
Performance:      319.865        0.075
1803
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1.tpr, VERSION 2019.1 (double precision)
1804
Can not increase nstlist because an NVE ensemble is used
1805
Using 1 MPI process
1806
Using 1 OpenMP thread 
1807

    
1808

    
1809
NOTE: Thread affinity was not set.
1810
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_normal.trr'
1811

    
1812
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
1813

    
1814
NOTE: 13 % of the run time was spent in pair search,
1815
      you might want to increase nstlist (this has no effect on accuracy)
1816

    
1817
               Core t (s)   Wall t (s)        (%)
1818
       Time:        0.001        0.001       96.7
1819
                 (ns/day)    (hour/ns)
1820
Performance:     1253.427        0.019
1821
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_normal.edr as double precision energy file
1822
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_rerun.edr as double precision energy file
1823
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
1824

    
1825
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (120 ms)
1826
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2
1827

    
1828
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp, line 42]:
1829
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
1830
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
1831
  scheme was introduced, but the group scheme was still the default. The
1832
  default is now the Verlet scheme, so you will observe different behaviour.
1833

    
1834

    
1835
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
1836
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
1837
  that with the Verlet scheme, nstlist has no effect on the accuracy of
1838
  your simulation.
1839

    
1840

    
1841
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
1842
  Setting nstcalcenergy (100) equal to nstenergy (4)
1843

    
1844
Generated 2485 of the 2485 non-bonded parameter combinations
1845
Generating 1-4 interactions: fudge = 0.5
1846
Generated 2485 of the 2485 1-4 parameter combinations
1847
Excluding 3 bonded neighbours molecule type 'nonanol'
1848
turning H bonds into constraints...
1849
Excluding 2 bonded neighbours molecule type 'SOL'
1850
turning H bonds into constraints...
1851
Removing all charge groups because cutoff-scheme=Verlet
1852
Number of degrees of freedom in T-Coupling group System is 79.00
1853

    
1854
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
1855
  NVE simulation: will use the initial temperature of 293.480 K for
1856
  determining the Verlet buffer size
1857

    
1858
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
1859
Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
1860
Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
1861
Note that mdrun will redetermine rlist based on the actual pair-list setup
1862

    
1863
NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
1864
  You are using a plain Coulomb cut-off, which might produce artifacts.
1865
  You might want to consider using PME electrostatics.
1866

    
1867

    
1868
This run will generate roughly 0 Mb of data
1869

    
1870
There were 5 notes
1871
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2.tpr, VERSION 2019.1 (double precision)
1872
Can not increase nstlist because an NVE ensemble is used
1873
Using 1 MPI process
1874
Using 1 OpenMP thread 
1875

    
1876

    
1877
NOTE: Thread affinity was not set.
1878
starting mdrun '30 system in water'
1879
16 steps,      0.0 ps.
1880

    
1881
Writing final coordinates.
1882

    
1883
               Core t (s)   Wall t (s)        (%)
1884
       Time:        0.005        0.005       98.6
1885
                 (ns/day)    (hour/ns)
1886
Performance:      303.597        0.079
1887
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2.tpr, VERSION 2019.1 (double precision)
1888
Can not increase nstlist because an NVE ensemble is used
1889
Using 1 MPI process
1890
Using 1 OpenMP thread 
1891

    
1892

    
1893
NOTE: Thread affinity was not set.
1894
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_normal.trr'
1895

    
1896
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
1897

    
1898
NOTE: 12 % of the run time was spent in pair search,
1899
      you might want to increase nstlist (this has no effect on accuracy)
1900

    
1901
               Core t (s)   Wall t (s)        (%)
1902
       Time:        0.001        0.001       96.7
1903
                 (ns/day)    (hour/ns)
1904
Performance:     1062.904        0.023
1905
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_normal.edr as double precision energy file
1906
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_rerun.edr as double precision energy file
1907
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
1908

    
1909
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (117 ms)
1910
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3
1911

    
1912
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp, line 42]:
1913
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
1914
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
1915
  scheme was introduced, but the group scheme was still the default. The
1916
  default is now the Verlet scheme, so you will observe different behaviour.
1917

    
1918

    
1919
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
1920
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
1921
  that with the Verlet scheme, nstlist has no effect on the accuracy of
1922
  your simulation.
1923

    
1924

    
1925
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
1926
  Setting nstcalcenergy (100) equal to nstenergy (4)
1927

    
1928
Generated 2485 of the 2485 non-bonded parameter combinations
1929
Generating 1-4 interactions: fudge = 0.5
1930
Generated 2485 of the 2485 1-4 parameter combinations
1931
Excluding 3 bonded neighbours molecule type 'nonanol'
1932
turning H bonds into constraints...
1933
Excluding 2 bonded neighbours molecule type 'SOL'
1934
turning H bonds into constraints...
1935
Removing all charge groups because cutoff-scheme=Verlet
1936
Number of degrees of freedom in T-Coupling group System is 79.00
1937

    
1938
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
1939
  NVE simulation: will use the initial temperature of 293.480 K for
1940
  determining the Verlet buffer size
1941

    
1942
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
1943
Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
1944
Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
1945
Note that mdrun will redetermine rlist based on the actual pair-list setup
1946

    
1947
NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
1948
  You are using a plain Coulomb cut-off, which might produce artifacts.
1949
  You might want to consider using PME electrostatics.
1950

    
1951

    
1952
This run will generate roughly 0 Mb of data
1953

    
1954
There were 5 notes
1955
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3.tpr, VERSION 2019.1 (double precision)
1956
Can not increase nstlist because an NVE ensemble is used
1957
Using 1 MPI process
1958
Using 1 OpenMP thread 
1959

    
1960

    
1961
NOTE: Thread affinity was not set.
1962
starting mdrun '30 system in water'
1963
16 steps,      0.0 ps.
1964

    
1965
Writing final coordinates.
1966

    
1967
               Core t (s)   Wall t (s)        (%)
1968
       Time:        0.005        0.005       98.5
1969
                 (ns/day)    (hour/ns)
1970
Performance:      272.556        0.088
1971
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3.tpr, VERSION 2019.1 (double precision)
1972
Can not increase nstlist because an NVE ensemble is used
1973
Using 1 MPI process
1974
Using 1 OpenMP thread 
1975

    
1976

    
1977
NOTE: Thread affinity was not set.
1978
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_normal.trr'
1979

    
1980
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
1981

    
1982
NOTE: 13 % of the run time was spent in pair search,
1983
      you might want to increase nstlist (this has no effect on accuracy)
1984

    
1985
               Core t (s)   Wall t (s)        (%)
1986
       Time:        0.001        0.002       96.6
1987
                 (ns/day)    (hour/ns)
1988
Performance:      974.932        0.025
1989
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_normal.edr as double precision energy file
1990
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_rerun.edr as double precision energy file
1991
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
1992

    
1993
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (138 ms)
1994
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4
1995

    
1996
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp, line 42]:
1997
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
1998
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
1999
  scheme was introduced, but the group scheme was still the default. The
2000
  default is now the Verlet scheme, so you will observe different behaviour.
2001

    
2002

    
2003
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
2004
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
2005
  that with the Verlet scheme, nstlist has no effect on the accuracy of
2006
  your simulation.
2007

    
2008

    
2009
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
2010
  Setting nstcalcenergy (100) equal to nstenergy (4)
2011

    
2012
Generated 2485 of the 2485 non-bonded parameter combinations
2013
Generating 1-4 interactions: fudge = 0.5
2014
Generated 2485 of the 2485 1-4 parameter combinations
2015
Excluding 3 bonded neighbours molecule type 'nonanol'
2016
turning H bonds into constraints...
2017
Excluding 2 bonded neighbours molecule type 'SOL'
2018
turning H bonds into constraints...
2019
Removing all charge groups because cutoff-scheme=Verlet
2020
Number of degrees of freedom in T-Coupling group System is 79.00
2021

    
2022
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
2023
  NVE simulation: will use the initial temperature of 293.480 K for
2024
  determining the Verlet buffer size
2025

    
2026
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
2027
Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
2028
Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
2029
Note that mdrun will redetermine rlist based on the actual pair-list setup
2030

    
2031
NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
2032
  You are using a plain Coulomb cut-off, which might produce artifacts.
2033
  You might want to consider using PME electrostatics.
2034

    
2035

    
2036
This run will generate roughly 0 Mb of data
2037

    
2038
There were 5 notes
2039
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4.tpr, VERSION 2019.1 (double precision)
2040
Can not increase nstlist because an NVE ensemble is used
2041
Using 1 MPI process
2042
Using 1 OpenMP thread 
2043

    
2044

    
2045
NOTE: Thread affinity was not set.
2046
starting mdrun '30 system in water'
2047
16 steps,      0.0 ps.
2048

    
2049
Writing final coordinates.
2050

    
2051
               Core t (s)   Wall t (s)        (%)
2052
       Time:        0.005        0.005       98.4
2053
                 (ns/day)    (hour/ns)
2054
Performance:      268.904        0.089
2055
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4.tpr, VERSION 2019.1 (double precision)
2056
Can not increase nstlist because an NVE ensemble is used
2057
Using 1 MPI process
2058
Using 1 OpenMP thread 
2059

    
2060

    
2061
NOTE: Thread affinity was not set.
2062
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_normal.trr'
2063

    
2064
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
2065

    
2066
NOTE: 12 % of the run time was spent in pair search,
2067
      you might want to increase nstlist (this has no effect on accuracy)
2068

    
2069
               Core t (s)   Wall t (s)        (%)
2070
       Time:        0.001        0.002       96.6
2071
                 (ns/day)    (hour/ns)
2072
Performance:      971.856        0.025
2073
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_normal.edr as double precision energy file
2074
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_rerun.edr as double precision energy file
2075
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
2076

    
2077
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (142 ms)
2078
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5
2079

    
2080
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp, line 42]:
2081
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
2082
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
2083
  scheme was introduced, but the group scheme was still the default. The
2084
  default is now the Verlet scheme, so you will observe different behaviour.
2085

    
2086

    
2087
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
2088
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
2089
  that with the Verlet scheme, nstlist has no effect on the accuracy of
2090
  your simulation.
2091

    
2092

    
2093
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
2094
  Setting nstcalcenergy (100) equal to nstenergy (4)
2095

    
2096
Generated 2485 of the 2485 non-bonded parameter combinations
2097
Generating 1-4 interactions: fudge = 0.5
2098
Generated 2485 of the 2485 1-4 parameter combinations
2099
Excluding 3 bonded neighbours molecule type 'nonanol'
2100
turning H bonds into constraints...
2101
Excluding 2 bonded neighbours molecule type 'SOL'
2102
turning H bonds into constraints...
2103
Removing all charge groups because cutoff-scheme=Verlet
2104
Number of degrees of freedom in T-Coupling group System is 79.00
2105

    
2106
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
2107
  NVE simulation: will use the initial temperature of 293.480 K for
2108
  determining the Verlet buffer size
2109

    
2110
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
2111
Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
2112
Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
2113
Note that mdrun will redetermine rlist based on the actual pair-list setup
2114

    
2115
NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
2116
  You are using a plain Coulomb cut-off, which might produce artifacts.
2117
  You might want to consider using PME electrostatics.
2118

    
2119

    
2120
This run will generate roughly 0 Mb of data
2121

    
2122
There were 5 notes
2123
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5.tpr, VERSION 2019.1 (double precision)
2124
Can not increase nstlist because an NVE ensemble is used
2125
Using 1 MPI process
2126
Using 1 OpenMP thread 
2127

    
2128

    
2129
NOTE: Thread affinity was not set.
2130
starting mdrun '30 system in water'
2131
16 steps,      0.0 ps.
2132

    
2133
Writing final coordinates.
2134

    
2135
               Core t (s)   Wall t (s)        (%)
2136
       Time:        0.005        0.005       98.4
2137
                 (ns/day)    (hour/ns)
2138
Performance:      270.036        0.089
2139
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5.tpr, VERSION 2019.1 (double precision)
2140
Can not increase nstlist because an NVE ensemble is used
2141
Using 1 MPI process
2142
Using 1 OpenMP thread 
2143

    
2144

    
2145
NOTE: Thread affinity was not set.
2146
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_normal.trr'
2147

    
2148
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
2149

    
2150
NOTE: 13 % of the run time was spent in pair search,
2151
      you might want to increase nstlist (this has no effect on accuracy)
2152

    
2153
               Core t (s)   Wall t (s)        (%)
2154
       Time:        0.001        0.002       96.5
2155
                 (ns/day)    (hour/ns)
2156
Performance:      975.086        0.025
2157
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_normal.edr as double precision energy file
2158
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_rerun.edr as double precision energy file
2159
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
2160

    
2161
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (147 ms)
2162
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6
2163

    
2164
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp, line 42]:
2165
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
2166
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
2167
  scheme was introduced, but the group scheme was still the default. The
2168
  default is now the Verlet scheme, so you will observe different behaviour.
2169

    
2170

    
2171
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
2172
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
2173
  that with the Verlet scheme, nstlist has no effect on the accuracy of
2174
  your simulation.
2175

    
2176

    
2177
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
2178
  Setting nstcalcenergy (100) equal to nstenergy (4)
2179

    
2180
Generated 2485 of the 2485 non-bonded parameter combinations
2181
Generating 1-4 interactions: fudge = 0.5
2182
Generated 2485 of the 2485 1-4 parameter combinations
2183
Excluding 3 bonded neighbours molecule type 'nonanol'
2184
turning H bonds into constraints...
2185
Excluding 2 bonded neighbours molecule type 'SOL'
2186
turning H bonds into constraints...
2187
Removing all charge groups because cutoff-scheme=Verlet
2188
Number of degrees of freedom in T-Coupling group System is 79.00
2189

    
2190
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
2191
  NVE simulation: will use the initial temperature of 293.480 K for
2192
  determining the Verlet buffer size
2193

    
2194
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
2195
Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
2196
Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
2197
Note that mdrun will redetermine rlist based on the actual pair-list setup
2198

    
2199
NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
2200
  You are using a plain Coulomb cut-off, which might produce artifacts.
2201
  You might want to consider using PME electrostatics.
2202

    
2203

    
2204
This run will generate roughly 0 Mb of data
2205

    
2206
There were 5 notes
2207
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6.tpr, VERSION 2019.1 (double precision)
2208
Can not increase nstlist because an NVE ensemble is used
2209
Using 1 MPI process
2210
Using 1 OpenMP thread 
2211

    
2212

    
2213
NOTE: Thread affinity was not set.
2214
starting mdrun '30 system in water'
2215
16 steps,      0.0 ps.
2216

    
2217
Writing final coordinates.
2218

    
2219
               Core t (s)   Wall t (s)        (%)
2220
       Time:        0.006        0.006       98.5
2221
                 (ns/day)    (hour/ns)
2222
Performance:      257.798        0.093
2223
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6.tpr, VERSION 2019.1 (double precision)
2224
Can not increase nstlist because an NVE ensemble is used
2225
Using 1 MPI process
2226
Using 1 OpenMP thread 
2227

    
2228

    
2229
NOTE: Thread affinity was not set.
2230
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_normal.trr'
2231

    
2232
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
2233

    
2234
NOTE: 13 % of the run time was spent in pair search,
2235
      you might want to increase nstlist (this has no effect on accuracy)
2236

    
2237
               Core t (s)   Wall t (s)        (%)
2238
       Time:        0.001        0.002       96.5
2239
                 (ns/day)    (hour/ns)
2240
Performance:      974.161        0.025
2241
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_normal.edr as double precision energy file
2242
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_rerun.edr as double precision energy file
2243
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
2244

    
2245
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (142 ms)
2246
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7
2247

    
2248
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp, line 42]:
2249
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
2250
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
2251
  scheme was introduced, but the group scheme was still the default. The
2252
  default is now the Verlet scheme, so you will observe different behaviour.
2253

    
2254

    
2255
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
2256
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
2257
  that with the Verlet scheme, nstlist has no effect on the accuracy of
2258
  your simulation.
2259

    
2260

    
2261
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
2262
  Setting nstcalcenergy (100) equal to nstenergy (4)
2263

    
2264
Generated 2485 of the 2485 non-bonded parameter combinations
2265
Generating 1-4 interactions: fudge = 0.5
2266
Generated 2485 of the 2485 1-4 parameter combinations
2267
Excluding 3 bonded neighbours molecule type 'nonanol'
2268
turning H bonds into constraints...
2269
Excluding 2 bonded neighbours molecule type 'SOL'
2270
turning H bonds into constraints...
2271
Removing all charge groups because cutoff-scheme=Verlet
2272
Number of degrees of freedom in T-Coupling group System is 79.00
2273

    
2274
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
2275
  NVE simulation: will use the initial temperature of 293.480 K for
2276
  determining the Verlet buffer size
2277

    
2278
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
2279
Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
2280
Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
2281
Note that mdrun will redetermine rlist based on the actual pair-list setup
2282

    
2283
NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
2284
  You are using a plain Coulomb cut-off, which might produce artifacts.
2285
  You might want to consider using PME electrostatics.
2286

    
2287

    
2288
This run will generate roughly 0 Mb of data
2289

    
2290
There were 5 notes
2291
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7.tpr, VERSION 2019.1 (double precision)
2292
Can not increase nstlist because an NVE ensemble is used
2293
Using 1 MPI process
2294
Using 1 OpenMP thread 
2295

    
2296

    
2297
NOTE: Thread affinity was not set.
2298
starting mdrun '30 system in water'
2299
16 steps,      0.0 ps.
2300

    
2301
Writing final coordinates.
2302

    
2303
               Core t (s)   Wall t (s)        (%)
2304
       Time:        0.005        0.006       98.4
2305
                 (ns/day)    (hour/ns)
2306
Performance:      266.565        0.090
2307
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7.tpr, VERSION 2019.1 (double precision)
2308
Can not increase nstlist because an NVE ensemble is used
2309
Using 1 MPI process
2310
Using 1 OpenMP thread 
2311

    
2312

    
2313
NOTE: Thread affinity was not set.
2314
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_normal.trr'
2315

    
2316
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
2317

    
2318
NOTE: 15 % of the run time was spent in pair search,
2319
      you might want to increase nstlist (this has no effect on accuracy)
2320

    
2321
               Core t (s)   Wall t (s)        (%)
2322
       Time:        0.001        0.002       95.8
2323
                 (ns/day)    (hour/ns)
2324
Performance:      954.687        0.025
2325
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_normal.edr as double precision energy file
2326
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_rerun.edr as double precision energy file
2327
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
2328

    
2329
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (138 ms)
2330
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8
2331

    
2332
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp, line 42]:
2333
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
2334
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
2335
  scheme was introduced, but the group scheme was still the default. The
2336
  default is now the Verlet scheme, so you will observe different behaviour.
2337

    
2338

    
2339
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
2340
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
2341
  that with the Verlet scheme, nstlist has no effect on the accuracy of
2342
  your simulation.
2343

    
2344

    
2345
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
2346
  Setting nstcalcenergy (100) equal to nstenergy (4)
2347

    
2348
Generated 2485 of the 2485 non-bonded parameter combinations
2349
Generating 1-4 interactions: fudge = 0.5
2350
Generated 2485 of the 2485 1-4 parameter combinations
2351
Excluding 3 bonded neighbours molecule type 'nonanol'
2352
turning H bonds into constraints...
2353
Excluding 2 bonded neighbours molecule type 'SOL'
2354
turning H bonds into constraints...
2355
Removing all charge groups because cutoff-scheme=Verlet
2356
Number of degrees of freedom in T-Coupling group System is 79.00
2357

    
2358
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
2359
  NVE simulation: will use the initial temperature of 293.480 K for
2360
  determining the Verlet buffer size
2361

    
2362
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
2363
Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
2364
Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
2365
Note that mdrun will redetermine rlist based on the actual pair-list setup
2366

    
2367
NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
2368
  You are using a plain Coulomb cut-off, which might produce artifacts.
2369
  You might want to consider using PME electrostatics.
2370

    
2371

    
2372
This run will generate roughly 0 Mb of data
2373

    
2374
There were 5 notes
2375
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8.tpr, VERSION 2019.1 (double precision)
2376
Can not increase nstlist because an NVE ensemble is used
2377
Using 1 MPI process
2378
Using 1 OpenMP thread 
2379

    
2380

    
2381
NOTE: Thread affinity was not set.
2382
starting mdrun '30 system in water'
2383
16 steps,      0.0 ps.
2384

    
2385
Writing final coordinates.
2386

    
2387
               Core t (s)   Wall t (s)        (%)
2388
       Time:        0.005        0.005       98.5
2389
                 (ns/day)    (hour/ns)
2390
Performance:      286.553        0.084
2391
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8.tpr, VERSION 2019.1 (double precision)
2392
Can not increase nstlist because an NVE ensemble is used
2393
Using 1 MPI process
2394
Using 1 OpenMP thread 
2395

    
2396

    
2397
NOTE: Thread affinity was not set.
2398
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_normal.trr'
2399

    
2400
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
2401

    
2402
NOTE: 17 % of the run time was spent in pair search,
2403
      you might want to increase nstlist (this has no effect on accuracy)
2404

    
2405
               Core t (s)   Wall t (s)        (%)
2406
       Time:        0.002        0.002       96.8
2407
                 (ns/day)    (hour/ns)
2408
Performance:      926.544        0.026
2409
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_normal.edr as double precision energy file
2410
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_rerun.edr as double precision energy file
2411
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
2412

    
2413
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (134 ms)
2414
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9
2415

    
2416
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp, line 42]:
2417
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
2418
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
2419
  scheme was introduced, but the group scheme was still the default. The
2420
  default is now the Verlet scheme, so you will observe different behaviour.
2421

    
2422

    
2423
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
2424
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
2425
  that with the Verlet scheme, nstlist has no effect on the accuracy of
2426
  your simulation.
2427

    
2428

    
2429
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
2430
  Setting nstcalcenergy (100) equal to nstenergy (4)
2431

    
2432
Generated 2485 of the 2485 non-bonded parameter combinations
2433
Generating 1-4 interactions: fudge = 0.5
2434
Generated 2485 of the 2485 1-4 parameter combinations
2435
Excluding 3 bonded neighbours molecule type 'nonanol'
2436
turning H bonds into constraints...
2437
Excluding 2 bonded neighbours molecule type 'SOL'
2438
turning H bonds into constraints...
2439
Removing all charge groups because cutoff-scheme=Verlet
2440
Number of degrees of freedom in T-Coupling group System is 79.00
2441

    
2442
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
2443
  NVE simulation: will use the initial temperature of 293.480 K for
2444
  determining the Verlet buffer size
2445

    
2446
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
2447
Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
2448
Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
2449
Note that mdrun will redetermine rlist based on the actual pair-list setup
2450

    
2451
NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
2452
  You are using a plain Coulomb cut-off, which might produce artifacts.
2453
  You might want to consider using PME electrostatics.
2454

    
2455

    
2456
This run will generate roughly 0 Mb of data
2457

    
2458
There were 5 notes
2459
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9.tpr, VERSION 2019.1 (double precision)
2460
Can not increase nstlist because an NVE ensemble is used
2461
Using 1 MPI process
2462
Using 1 OpenMP thread 
2463

    
2464

    
2465
NOTE: Thread affinity was not set.
2466
starting mdrun '30 system in water'
2467
16 steps,      0.0 ps.
2468

    
2469
Writing final coordinates.
2470

    
2471
               Core t (s)   Wall t (s)        (%)
2472
       Time:        0.005        0.006       98.4
2473
                 (ns/day)    (hour/ns)
2474
Performance:      263.939        0.091
2475
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9.tpr, VERSION 2019.1 (double precision)
2476
Can not increase nstlist because an NVE ensemble is used
2477
Using 1 MPI process
2478
Using 1 OpenMP thread 
2479

    
2480

    
2481
NOTE: Thread affinity was not set.
2482
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_normal.trr'
2483

    
2484
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
2485

    
2486
NOTE: 13 % of the run time was spent in pair search,
2487
      you might want to increase nstlist (this has no effect on accuracy)
2488

    
2489
               Core t (s)   Wall t (s)        (%)
2490
       Time:        0.001        0.002       96.6
2491
                 (ns/day)    (hour/ns)
2492
Performance:      976.632        0.025
2493
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_normal.edr as double precision energy file
2494
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_rerun.edr as double precision energy file
2495
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
2496

    
2497
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (134 ms)
2498
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10
2499

    
2500
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp, line 42]:
2501
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
2502
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
2503
  scheme was introduced, but the group scheme was still the default. The
2504
  default is now the Verlet scheme, so you will observe different behaviour.
2505

    
2506

    
2507
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
2508
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
2509
  that with the Verlet scheme, nstlist has no effect on the accuracy of
2510
  your simulation.
2511

    
2512

    
2513
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
2514
  Setting nstcalcenergy (100) equal to nstenergy (4)
2515

    
2516
Generated 2485 of the 2485 non-bonded parameter combinations
2517
Generating 1-4 interactions: fudge = 0.5
2518
Generated 2485 of the 2485 1-4 parameter combinations
2519
Excluding 3 bonded neighbours molecule type 'nonanol'
2520
turning H bonds into constraints...
2521
Excluding 2 bonded neighbours molecule type 'SOL'
2522
turning H bonds into constraints...
2523
Removing all charge groups because cutoff-scheme=Verlet
2524
Number of degrees of freedom in T-Coupling group System is 79.00
2525

    
2526
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
2527
  NVE simulation: will use the initial temperature of 293.480 K for
2528
  determining the Verlet buffer size
2529

    
2530
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
2531
Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
2532
Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
2533
Note that mdrun will redetermine rlist based on the actual pair-list setup
2534

    
2535
NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
2536
  You are using a plain Coulomb cut-off, which might produce artifacts.
2537
  You might want to consider using PME electrostatics.
2538

    
2539

    
2540
This run will generate roughly 0 Mb of data
2541

    
2542
There were 5 notes
2543
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10.tpr, VERSION 2019.1 (double precision)
2544
Can not increase nstlist because an NVE ensemble is used
2545
Using 1 MPI process
2546
Using 1 OpenMP thread 
2547

    
2548

    
2549
NOTE: Thread affinity was not set.
2550
starting mdrun '30 system in water'
2551
16 steps,      0.0 ps.
2552

    
2553
Writing final coordinates.
2554

    
2555
               Core t (s)   Wall t (s)        (%)
2556
       Time:        0.005        0.005       98.4
2557
                 (ns/day)    (hour/ns)
2558
Performance:      273.379        0.088
2559
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10.tpr, VERSION 2019.1 (double precision)
2560
Can not increase nstlist because an NVE ensemble is used
2561
Using 1 MPI process
2562
Using 1 OpenMP thread 
2563

    
2564

    
2565
NOTE: Thread affinity was not set.
2566
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_normal.trr'
2567

    
2568
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
2569

    
2570
NOTE: 13 % of the run time was spent in pair search,
2571
      you might want to increase nstlist (this has no effect on accuracy)
2572

    
2573
               Core t (s)   Wall t (s)        (%)
2574
       Time:        0.001        0.001       96.6
2575
                 (ns/day)    (hour/ns)
2576
Performance:     1048.790        0.023
2577
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_normal.edr as double precision energy file
2578
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_rerun.edr as double precision energy file
2579
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
2580

    
2581
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (139 ms)
2582
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11
2583

    
2584
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp, line 42]:
2585
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
2586
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
2587
  scheme was introduced, but the group scheme was still the default. The
2588
  default is now the Verlet scheme, so you will observe different behaviour.
2589

    
2590

    
2591
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
2592
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
2593
  that with the Verlet scheme, nstlist has no effect on the accuracy of
2594
  your simulation.
2595

    
2596

    
2597
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
2598
  Setting nstcalcenergy (100) equal to nstenergy (4)
2599

    
2600
Generated 2485 of the 2485 non-bonded parameter combinations
2601
Generating 1-4 interactions: fudge = 0.5
2602
Generated 2485 of the 2485 1-4 parameter combinations
2603
Excluding 3 bonded neighbours molecule type 'nonanol'
2604
turning H bonds into constraints...
2605
Excluding 2 bonded neighbours molecule type 'SOL'
2606
turning H bonds into constraints...
2607
Removing all charge groups because cutoff-scheme=Verlet
2608
Number of degrees of freedom in T-Coupling group System is 79.00
2609

    
2610
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
2611
  NVE simulation: will use the initial temperature of 293.480 K for
2612
  determining the Verlet buffer size
2613

    
2614
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
2615
Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
2616
Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
2617
Note that mdrun will redetermine rlist based on the actual pair-list setup
2618

    
2619
NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
2620
  You are using a plain Coulomb cut-off, which might produce artifacts.
2621
  You might want to consider using PME electrostatics.
2622

    
2623

    
2624
This run will generate roughly 0 Mb of data
2625

    
2626
There were 5 notes
2627
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11.tpr, VERSION 2019.1 (double precision)
2628
Can not increase nstlist because an NVE ensemble is used
2629
Using 1 MPI process
2630
Using 1 OpenMP thread 
2631

    
2632

    
2633
NOTE: Thread affinity was not set.
2634
starting mdrun '30 system in water'
2635
16 steps,      0.0 ps.
2636

    
2637
Writing final coordinates.
2638

    
2639
               Core t (s)   Wall t (s)        (%)
2640
       Time:        0.005        0.006       98.1
2641
                 (ns/day)    (hour/ns)
2642
Performance:      262.701        0.091
2643
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11.tpr, VERSION 2019.1 (double precision)
2644
Can not increase nstlist because an NVE ensemble is used
2645
Using 1 MPI process
2646
Using 1 OpenMP thread 
2647

    
2648

    
2649
NOTE: Thread affinity was not set.
2650
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_normal.trr'
2651

    
2652
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
2653

    
2654
NOTE: 13 % of the run time was spent in pair search,
2655
      you might want to increase nstlist (this has no effect on accuracy)
2656

    
2657
               Core t (s)   Wall t (s)        (%)
2658
       Time:        0.001        0.002       96.6
2659
                 (ns/day)    (hour/ns)
2660
Performance:      969.409        0.025
2661
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_normal.edr as double precision energy file
2662
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_rerun.edr as double precision energy file
2663
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
2664

    
2665
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (139 ms)
2666
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12
2667

    
2668
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp, line 42]:
2669
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
2670
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
2671
  scheme was introduced, but the group scheme was still the default. The
2672
  default is now the Verlet scheme, so you will observe different behaviour.
2673

    
2674

    
2675
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
2676
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
2677
  that with the Verlet scheme, nstlist has no effect on the accuracy of
2678
  your simulation.
2679

    
2680

    
2681
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
2682
  Setting nstcalcenergy (100) equal to nstenergy (4)
2683

    
2684
Generated 2485 of the 2485 non-bonded parameter combinations
2685
Generating 1-4 interactions: fudge = 0.5
2686
Generated 2485 of the 2485 1-4 parameter combinations
2687
Excluding 3 bonded neighbours molecule type 'nonanol'
2688
turning H bonds into constraints...
2689
Excluding 2 bonded neighbours molecule type 'SOL'
2690
turning H bonds into constraints...
2691
Removing all charge groups because cutoff-scheme=Verlet
2692
Number of degrees of freedom in T-Coupling group System is 79.00
2693

    
2694
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
2695
  NVE simulation: will use the initial temperature of 293.480 K for
2696
  determining the Verlet buffer size
2697

    
2698
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
2699
Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
2700
Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
2701
Note that mdrun will redetermine rlist based on the actual pair-list setup
2702

    
2703
NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
2704
  You are using a plain Coulomb cut-off, which might produce artifacts.
2705
  You might want to consider using PME electrostatics.
2706

    
2707

    
2708
This run will generate roughly 0 Mb of data
2709

    
2710
There were 5 notes
2711
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12.tpr, VERSION 2019.1 (double precision)
2712
Can not increase nstlist because an NVE ensemble is used
2713
Using 1 MPI process
2714
Using 1 OpenMP thread 
2715

    
2716

    
2717
NOTE: Thread affinity was not set.
2718
starting mdrun '30 system in water'
2719
16 steps,      0.0 ps.
2720

    
2721
Writing final coordinates.
2722

    
2723
               Core t (s)   Wall t (s)        (%)
2724
       Time:        0.006        0.006       98.5
2725
                 (ns/day)    (hour/ns)
2726
Performance:      260.744        0.092
2727
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12.tpr, VERSION 2019.1 (double precision)
2728
Can not increase nstlist because an NVE ensemble is used
2729
Using 1 MPI process
2730
Using 1 OpenMP thread 
2731

    
2732

    
2733
NOTE: Thread affinity was not set.
2734
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_normal.trr'
2735

    
2736
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
2737

    
2738
NOTE: 12 % of the run time was spent in pair search,
2739
      you might want to increase nstlist (this has no effect on accuracy)
2740

    
2741
               Core t (s)   Wall t (s)        (%)
2742
       Time:        0.001        0.001       96.8
2743
                 (ns/day)    (hour/ns)
2744
Performance:     1047.008        0.023
2745
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_normal.edr as double precision energy file
2746
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_rerun.edr as double precision energy file
2747
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
2748

    
2749
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (139 ms)
2750
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13
2751

    
2752
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp, line 42]:
2753
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
2754
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
2755
  scheme was introduced, but the group scheme was still the default. The
2756
  default is now the Verlet scheme, so you will observe different behaviour.
2757

    
2758

    
2759
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
2760
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
2761
  that with the Verlet scheme, nstlist has no effect on the accuracy of
2762
  your simulation.
2763

    
2764

    
2765
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
2766
  Setting nstcalcenergy (100) equal to nstenergy (4)
2767

    
2768
Generated 2485 of the 2485 non-bonded parameter combinations
2769
Generating 1-4 interactions: fudge = 0.5
2770
Generated 2485 of the 2485 1-4 parameter combinations
2771
Excluding 3 bonded neighbours molecule type 'nonanol'
2772
turning H bonds into constraints...
2773
Excluding 2 bonded neighbours molecule type 'SOL'
2774
turning H bonds into constraints...
2775
Removing all charge groups because cutoff-scheme=Verlet
2776
Number of degrees of freedom in T-Coupling group System is 79.00
2777

    
2778
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
2779
  NVE simulation: will use the initial temperature of 293.480 K for
2780
  determining the Verlet buffer size
2781

    
2782
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
2783
Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
2784
Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
2785
Note that mdrun will redetermine rlist based on the actual pair-list setup
2786

    
2787
NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
2788
  You are using a plain Coulomb cut-off, which might produce artifacts.
2789
  You might want to consider using PME electrostatics.
2790

    
2791

    
2792
This run will generate roughly 0 Mb of data
2793

    
2794
There were 5 notes
2795
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13.tpr, VERSION 2019.1 (double precision)
2796
Can not increase nstlist because an NVE ensemble is used
2797
Using 1 MPI process
2798
Using 1 OpenMP thread 
2799

    
2800

    
2801
NOTE: Thread affinity was not set.
2802
starting mdrun '30 system in water'
2803
16 steps,      0.0 ps.
2804

    
2805
Writing final coordinates.
2806

    
2807
               Core t (s)   Wall t (s)        (%)
2808
       Time:        0.006        0.006       98.5
2809
                 (ns/day)    (hour/ns)
2810
Performance:      253.429        0.095
2811
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13.tpr, VERSION 2019.1 (double precision)
2812
Can not increase nstlist because an NVE ensemble is used
2813
Using 1 MPI process
2814
Using 1 OpenMP thread 
2815

    
2816

    
2817
NOTE: Thread affinity was not set.
2818
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_normal.trr'
2819

    
2820
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
2821

    
2822
NOTE: 13 % of the run time was spent in pair search,
2823
      you might want to increase nstlist (this has no effect on accuracy)
2824

    
2825
               Core t (s)   Wall t (s)        (%)
2826
       Time:        0.001        0.002       95.6
2827
                 (ns/day)    (hour/ns)
2828
Performance:      963.798        0.025
2829
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_normal.edr as double precision energy file
2830
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_rerun.edr as double precision energy file
2831
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
2832

    
2833
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (140 ms)
2834
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14
2835

    
2836
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp, line 42]:
2837
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
2838
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
2839
  scheme was introduced, but the group scheme was still the default. The
2840
  default is now the Verlet scheme, so you will observe different behaviour.
2841

    
2842

    
2843
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
2844
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
2845
  that with the Verlet scheme, nstlist has no effect on the accuracy of
2846
  your simulation.
2847

    
2848

    
2849
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
2850
  Setting nstcalcenergy (100) equal to nstenergy (4)
2851

    
2852
Generated 2485 of the 2485 non-bonded parameter combinations
2853
Generating 1-4 interactions: fudge = 0.5
2854
Generated 2485 of the 2485 1-4 parameter combinations
2855
Excluding 3 bonded neighbours molecule type 'nonanol'
2856
turning H bonds into constraints...
2857
Excluding 2 bonded neighbours molecule type 'SOL'
2858
turning H bonds into constraints...
2859
Removing all charge groups because cutoff-scheme=Verlet
2860
Number of degrees of freedom in T-Coupling group System is 79.00
2861

    
2862
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
2863
  NVE simulation: will use the initial temperature of 293.480 K for
2864
  determining the Verlet buffer size
2865

    
2866
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
2867
Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
2868
Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
2869
Note that mdrun will redetermine rlist based on the actual pair-list setup
2870

    
2871
NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
2872
  You are using a plain Coulomb cut-off, which might produce artifacts.
2873
  You might want to consider using PME electrostatics.
2874

    
2875

    
2876
This run will generate roughly 0 Mb of data
2877

    
2878
There were 5 notes
2879
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14.tpr, VERSION 2019.1 (double precision)
2880
Can not increase nstlist because an NVE ensemble is used
2881
Using 1 MPI process
2882
Using 1 OpenMP thread 
2883

    
2884

    
2885
NOTE: Thread affinity was not set.
2886
starting mdrun '30 system in water'
2887
16 steps,      0.0 ps.
2888

    
2889
Writing final coordinates.
2890

    
2891
               Core t (s)   Wall t (s)        (%)
2892
       Time:        0.006        0.006       98.5
2893
                 (ns/day)    (hour/ns)
2894
Performance:      257.141        0.093
2895
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14.tpr, VERSION 2019.1 (double precision)
2896
Can not increase nstlist because an NVE ensemble is used
2897
Using 1 MPI process
2898
Using 1 OpenMP thread 
2899

    
2900

    
2901
NOTE: Thread affinity was not set.
2902
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_normal.trr'
2903

    
2904
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
2905

    
2906
NOTE: 12 % of the run time was spent in pair search,
2907
      you might want to increase nstlist (this has no effect on accuracy)
2908

    
2909
               Core t (s)   Wall t (s)        (%)
2910
       Time:        0.001        0.001       96.0
2911
                 (ns/day)    (hour/ns)
2912
Performance:     1069.548        0.022
2913
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_normal.edr as double precision energy file
2914
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_rerun.edr as double precision energy file
2915
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
2916

    
2917
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (133 ms)
2918
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15
2919

    
2920
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp, line 42]:
2921
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
2922
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
2923
  scheme was introduced, but the group scheme was still the default. The
2924
  default is now the Verlet scheme, so you will observe different behaviour.
2925

    
2926

    
2927
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
2928
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
2929
  that with the Verlet scheme, nstlist has no effect on the accuracy of
2930
  your simulation.
2931

    
2932

    
2933
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
2934
  Setting nstcalcenergy (100) equal to nstenergy (4)
2935

    
2936
Generated 2485 of the 2485 non-bonded parameter combinations
2937
Generating 1-4 interactions: fudge = 0.5
2938
Generated 2485 of the 2485 1-4 parameter combinations
2939
Excluding 3 bonded neighbours molecule type 'nonanol'
2940
turning H bonds into constraints...
2941
Excluding 2 bonded neighbours molecule type 'SOL'
2942
turning H bonds into constraints...
2943
Removing all charge groups because cutoff-scheme=Verlet
2944
Number of degrees of freedom in T-Coupling group System is 79.00
2945

    
2946
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
2947
  NVE simulation: will use the initial temperature of 293.480 K for
2948
  determining the Verlet buffer size
2949

    
2950
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
2951
Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
2952
Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
2953
Note that mdrun will redetermine rlist based on the actual pair-list setup
2954

    
2955
NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
2956
  You are using a plain Coulomb cut-off, which might produce artifacts.
2957
  You might want to consider using PME electrostatics.
2958

    
2959

    
2960
This run will generate roughly 0 Mb of data
2961

    
2962
There were 5 notes
2963
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15.tpr, VERSION 2019.1 (double precision)
2964
Can not increase nstlist because an NVE ensemble is used
2965
Using 1 MPI process
2966
Using 1 OpenMP thread 
2967

    
2968

    
2969
NOTE: Thread affinity was not set.
2970
starting mdrun '30 system in water'
2971
16 steps,      0.0 ps.
2972

    
2973
Writing final coordinates.
2974

    
2975
               Core t (s)   Wall t (s)        (%)
2976
       Time:        0.005        0.005       98.3
2977
                 (ns/day)    (hour/ns)
2978
Performance:      273.731        0.088
2979
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15.tpr, VERSION 2019.1 (double precision)
2980
Can not increase nstlist because an NVE ensemble is used
2981
Using 1 MPI process
2982
Using 1 OpenMP thread 
2983

    
2984

    
2985
NOTE: Thread affinity was not set.
2986
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_normal.trr'
2987

    
2988
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
2989

    
2990
NOTE: 12 % of the run time was spent in pair search,
2991
      you might want to increase nstlist (this has no effect on accuracy)
2992

    
2993
               Core t (s)   Wall t (s)        (%)
2994
       Time:        0.001        0.001       96.6
2995
                 (ns/day)    (hour/ns)
2996
Performance:     1051.475        0.023
2997
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_normal.edr as double precision energy file
2998
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_rerun.edr as double precision energy file
2999
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
3000

    
3001
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (133 ms)
3002
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16
3003

    
3004
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp, line 42]:
3005
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
3006
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
3007
  scheme was introduced, but the group scheme was still the default. The
3008
  default is now the Verlet scheme, so you will observe different behaviour.
3009

    
3010

    
3011
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
3012
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
3013
  that with the Verlet scheme, nstlist has no effect on the accuracy of
3014
  your simulation.
3015

    
3016

    
3017
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
3018
  Setting nstcalcenergy (100) equal to nstenergy (4)
3019

    
3020
Generated 2485 of the 2485 non-bonded parameter combinations
3021
Generating 1-4 interactions: fudge = 0.5
3022
Generated 2485 of the 2485 1-4 parameter combinations
3023
Excluding 3 bonded neighbours molecule type 'nonanol'
3024
turning H bonds into constraints...
3025
Excluding 2 bonded neighbours molecule type 'SOL'
3026
turning H bonds into constraints...
3027
Removing all charge groups because cutoff-scheme=Verlet
3028
Number of degrees of freedom in T-Coupling group System is 79.00
3029

    
3030
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
3031
  NVE simulation: will use the initial temperature of 293.480 K for
3032
  determining the Verlet buffer size
3033

    
3034
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
3035
Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
3036
Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
3037
Note that mdrun will redetermine rlist based on the actual pair-list setup
3038

    
3039
NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
3040
  You are using a plain Coulomb cut-off, which might produce artifacts.
3041
  You might want to consider using PME electrostatics.
3042

    
3043

    
3044
This run will generate roughly 0 Mb of data
3045

    
3046
There were 5 notes
3047
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16.tpr, VERSION 2019.1 (double precision)
3048
Can not increase nstlist because an NVE ensemble is used
3049
Using 1 MPI process
3050
Using 1 OpenMP thread 
3051

    
3052

    
3053
NOTE: Thread affinity was not set.
3054
starting mdrun '30 system in water'
3055
16 steps,      0.0 ps.
3056

    
3057
Writing final coordinates.
3058

    
3059
               Core t (s)   Wall t (s)        (%)
3060
       Time:        0.005        0.005       98.5
3061
                 (ns/day)    (hour/ns)
3062
Performance:      302.375        0.079
3063
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16.tpr, VERSION 2019.1 (double precision)
3064
Can not increase nstlist because an NVE ensemble is used
3065
Using 1 MPI process
3066
Using 1 OpenMP thread 
3067

    
3068

    
3069
NOTE: Thread affinity was not set.
3070
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_normal.trr'
3071

    
3072
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
3073

    
3074
NOTE: 13 % of the run time was spent in pair search,
3075
      you might want to increase nstlist (this has no effect on accuracy)
3076

    
3077
               Core t (s)   Wall t (s)        (%)
3078
       Time:        0.001        0.001       96.6
3079
                 (ns/day)    (hour/ns)
3080
Performance:     1082.896        0.022
3081
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_normal.edr as double precision energy file
3082
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_rerun.edr as double precision energy file
3083
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
3084

    
3085
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (127 ms)
3086
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17
3087

    
3088
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp, line 42]:
3089
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
3090
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
3091
  scheme was introduced, but the group scheme was still the default. The
3092
  default is now the Verlet scheme, so you will observe different behaviour.
3093

    
3094

    
3095
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
3096
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
3097
  that with the Verlet scheme, nstlist has no effect on the accuracy of
3098
  your simulation.
3099

    
3100

    
3101
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
3102
  Setting nstcalcenergy (100) equal to nstenergy (4)
3103

    
3104
Generated 2485 of the 2485 non-bonded parameter combinations
3105
Generating 1-4 interactions: fudge = 0.5
3106
Generated 2485 of the 2485 1-4 parameter combinations
3107
Excluding 3 bonded neighbours molecule type 'nonanol'
3108
turning H bonds into constraints...
3109
Excluding 2 bonded neighbours molecule type 'SOL'
3110
turning H bonds into constraints...
3111
Removing all charge groups because cutoff-scheme=Verlet
3112
Number of degrees of freedom in T-Coupling group System is 79.00
3113

    
3114
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
3115
  NVE simulation: will use the initial temperature of 293.480 K for
3116
  determining the Verlet buffer size
3117

    
3118
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
3119
Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
3120
Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
3121
Note that mdrun will redetermine rlist based on the actual pair-list setup
3122

    
3123
NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
3124
  You are using a plain Coulomb cut-off, which might produce artifacts.
3125
  You might want to consider using PME electrostatics.
3126

    
3127

    
3128
This run will generate roughly 0 Mb of data
3129

    
3130
There were 5 notes
3131
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17.tpr, VERSION 2019.1 (double precision)
3132
Can not increase nstlist because an NVE ensemble is used
3133
Using 1 MPI process
3134
Using 1 OpenMP thread 
3135

    
3136

    
3137
NOTE: Thread affinity was not set.
3138
starting mdrun '30 system in water'
3139
16 steps,      0.0 ps.
3140

    
3141
Writing final coordinates.
3142

    
3143
               Core t (s)   Wall t (s)        (%)
3144
       Time:        0.006        0.006       98.5
3145
                 (ns/day)    (hour/ns)
3146
Performance:      253.023        0.095
3147
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17.tpr, VERSION 2019.1 (double precision)
3148
Can not increase nstlist because an NVE ensemble is used
3149
Using 1 MPI process
3150
Using 1 OpenMP thread 
3151

    
3152

    
3153
NOTE: Thread affinity was not set.
3154
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_normal.trr'
3155

    
3156
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
3157

    
3158
NOTE: 13 % of the run time was spent in pair search,
3159
      you might want to increase nstlist (this has no effect on accuracy)
3160

    
3161
               Core t (s)   Wall t (s)        (%)
3162
       Time:        0.001        0.002       96.6
3163
                 (ns/day)    (hour/ns)
3164
Performance:      966.519        0.025
3165
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_normal.edr as double precision energy file
3166
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_rerun.edr as double precision energy file
3167
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
3168

    
3169
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (140 ms)
3170
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18
3171

    
3172
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp, line 42]:
3173
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
3174
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
3175
  scheme was introduced, but the group scheme was still the default. The
3176
  default is now the Verlet scheme, so you will observe different behaviour.
3177

    
3178

    
3179
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
3180
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
3181
  that with the Verlet scheme, nstlist has no effect on the accuracy of
3182
  your simulation.
3183

    
3184

    
3185
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
3186
  Setting nstcalcenergy (100) equal to nstenergy (4)
3187

    
3188
Generated 2485 of the 2485 non-bonded parameter combinations
3189
Generating 1-4 interactions: fudge = 0.5
3190
Generated 2485 of the 2485 1-4 parameter combinations
3191
Excluding 3 bonded neighbours molecule type 'nonanol'
3192
turning H bonds into constraints...
3193
Excluding 2 bonded neighbours molecule type 'SOL'
3194
turning H bonds into constraints...
3195
Removing all charge groups because cutoff-scheme=Verlet
3196
Number of degrees of freedom in T-Coupling group System is 79.00
3197

    
3198
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
3199
  NVE simulation: will use the initial temperature of 293.480 K for
3200
  determining the Verlet buffer size
3201

    
3202
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
3203
Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
3204
Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
3205
Note that mdrun will redetermine rlist based on the actual pair-list setup
3206

    
3207
NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
3208
  You are using a plain Coulomb cut-off, which might produce artifacts.
3209
  You might want to consider using PME electrostatics.
3210

    
3211

    
3212
This run will generate roughly 0 Mb of data
3213

    
3214
There were 5 notes
3215
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18.tpr, VERSION 2019.1 (double precision)
3216
Can not increase nstlist because an NVE ensemble is used
3217
Using 1 MPI process
3218
Using 1 OpenMP thread 
3219

    
3220

    
3221
NOTE: Thread affinity was not set.
3222
starting mdrun '30 system in water'
3223
16 steps,      0.0 ps.
3224

    
3225
Writing final coordinates.
3226

    
3227
               Core t (s)   Wall t (s)        (%)
3228
       Time:        0.005        0.006       98.4
3229
                 (ns/day)    (hour/ns)
3230
Performance:      264.449        0.091
3231
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18.tpr, VERSION 2019.1 (double precision)
3232
Can not increase nstlist because an NVE ensemble is used
3233
Using 1 MPI process
3234
Using 1 OpenMP thread 
3235

    
3236

    
3237
NOTE: Thread affinity was not set.
3238
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_normal.trr'
3239

    
3240
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
3241

    
3242
NOTE: 17 % of the run time was spent in pair search,
3243
      you might want to increase nstlist (this has no effect on accuracy)
3244

    
3245
               Core t (s)   Wall t (s)        (%)
3246
       Time:        0.001        0.001       97.0
3247
                 (ns/day)    (hour/ns)
3248
Performance:     1008.776        0.024
3249
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_normal.edr as double precision energy file
3250
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_rerun.edr as double precision energy file
3251
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
3252

    
3253
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (139 ms)
3254
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19
3255

    
3256
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp, line 42]:
3257
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
3258
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
3259
  scheme was introduced, but the group scheme was still the default. The
3260
  default is now the Verlet scheme, so you will observe different behaviour.
3261

    
3262

    
3263
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
3264
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
3265
  that with the Verlet scheme, nstlist has no effect on the accuracy of
3266
  your simulation.
3267

    
3268

    
3269
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
3270
  Setting nstcalcenergy (100) equal to nstenergy (4)
3271

    
3272
Generated 2485 of the 2485 non-bonded parameter combinations
3273
Generating 1-4 interactions: fudge = 0.5
3274
Generated 2485 of the 2485 1-4 parameter combinations
3275
Excluding 3 bonded neighbours molecule type 'nonanol'
3276
turning H bonds into constraints...
3277
Excluding 2 bonded neighbours molecule type 'SOL'
3278
turning H bonds into constraints...
3279
Removing all charge groups because cutoff-scheme=Verlet
3280
Number of degrees of freedom in T-Coupling group System is 79.00
3281

    
3282
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
3283
  NVE simulation: will use the initial temperature of 293.480 K for
3284
  determining the Verlet buffer size
3285

    
3286
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
3287
Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
3288
Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
3289
Note that mdrun will redetermine rlist based on the actual pair-list setup
3290

    
3291
NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
3292
  You are using a plain Coulomb cut-off, which might produce artifacts.
3293
  You might want to consider using PME electrostatics.
3294

    
3295

    
3296
This run will generate roughly 0 Mb of data
3297

    
3298
There were 5 notes
3299
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19.tpr, VERSION 2019.1 (double precision)
3300
Can not increase nstlist because an NVE ensemble is used
3301
Using 1 MPI process
3302
Using 1 OpenMP thread 
3303

    
3304

    
3305
NOTE: Thread affinity was not set.
3306
starting mdrun '30 system in water'
3307
16 steps,      0.0 ps.
3308

    
3309
Writing final coordinates.
3310

    
3311
               Core t (s)   Wall t (s)        (%)
3312
       Time:        0.005        0.005       98.6
3313
                 (ns/day)    (hour/ns)
3314
Performance:      312.324        0.077
3315
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19.tpr, VERSION 2019.1 (double precision)
3316
Can not increase nstlist because an NVE ensemble is used
3317
Using 1 MPI process
3318
Using 1 OpenMP thread 
3319

    
3320

    
3321
NOTE: Thread affinity was not set.
3322
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_normal.trr'
3323

    
3324
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
3325

    
3326
NOTE: 13 % of the run time was spent in pair search,
3327
      you might want to increase nstlist (this has no effect on accuracy)
3328

    
3329
               Core t (s)   Wall t (s)        (%)
3330
       Time:        0.002        0.002       96.8
3331
                 (ns/day)    (hour/ns)
3332
Performance:      939.831        0.026
3333
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_normal.edr as double precision energy file
3334
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_rerun.edr as double precision energy file
3335
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
3336

    
3337
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (131 ms)
3338
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20
3339

    
3340
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp, line 42]:
3341
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
3342
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
3343
  scheme was introduced, but the group scheme was still the default. The
3344
  default is now the Verlet scheme, so you will observe different behaviour.
3345

    
3346

    
3347
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
3348
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
3349
  that with the Verlet scheme, nstlist has no effect on the accuracy of
3350
  your simulation.
3351

    
3352

    
3353
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
3354
  Setting nstcalcenergy (100) equal to nstenergy (4)
3355

    
3356
Generated 2485 of the 2485 non-bonded parameter combinations
3357
Generating 1-4 interactions: fudge = 0.5
3358
Generated 2485 of the 2485 1-4 parameter combinations
3359
Excluding 3 bonded neighbours molecule type 'nonanol'
3360
turning H bonds into constraints...
3361
Excluding 2 bonded neighbours molecule type 'SOL'
3362
turning H bonds into constraints...
3363
Removing all charge groups because cutoff-scheme=Verlet
3364
Number of degrees of freedom in T-Coupling group System is 79.00
3365

    
3366
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
3367
  NVE simulation: will use the initial temperature of 293.480 K for
3368
  determining the Verlet buffer size
3369

    
3370
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
3371
Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
3372
Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
3373
Note that mdrun will redetermine rlist based on the actual pair-list setup
3374

    
3375
NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
3376
  You are using a plain Coulomb cut-off, which might produce artifacts.
3377
  You might want to consider using PME electrostatics.
3378

    
3379

    
3380
This run will generate roughly 0 Mb of data
3381

    
3382
There were 5 notes
3383
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20.tpr, VERSION 2019.1 (double precision)
3384
Can not increase nstlist because an NVE ensemble is used
3385
Using 1 MPI process
3386
Using 1 OpenMP thread 
3387

    
3388

    
3389
NOTE: Thread affinity was not set.
3390
starting mdrun '30 system in water'
3391
16 steps,      0.0 ps.
3392

    
3393
Writing final coordinates.
3394

    
3395
               Core t (s)   Wall t (s)        (%)
3396
       Time:        0.006        0.006       98.4
3397
                 (ns/day)    (hour/ns)
3398
Performance:      259.711        0.092
3399
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20.tpr, VERSION 2019.1 (double precision)
3400
Can not increase nstlist because an NVE ensemble is used
3401
Using 1 MPI process
3402
Using 1 OpenMP thread 
3403

    
3404

    
3405
NOTE: Thread affinity was not set.
3406
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_normal.trr'
3407

    
3408
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
3409

    
3410
NOTE: 13 % of the run time was spent in pair search,
3411
      you might want to increase nstlist (this has no effect on accuracy)
3412

    
3413
               Core t (s)   Wall t (s)        (%)
3414
       Time:        0.001        0.001       96.7
3415
                 (ns/day)    (hour/ns)
3416
Performance:     1034.177        0.023
3417
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_normal.edr as double precision energy file
3418
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_rerun.edr as double precision energy file
3419
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
3420

    
3421
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (141 ms)
3422
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21
3423

    
3424
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp, line 42]:
3425
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
3426
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
3427
  scheme was introduced, but the group scheme was still the default. The
3428
  default is now the Verlet scheme, so you will observe different behaviour.
3429

    
3430

    
3431
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
3432
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
3433
  that with the Verlet scheme, nstlist has no effect on the accuracy of
3434
  your simulation.
3435

    
3436

    
3437
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
3438
  Setting nstcalcenergy (100) equal to nstenergy (4)
3439

    
3440
Generated 2485 of the 2485 non-bonded parameter combinations
3441
Generating 1-4 interactions: fudge = 0.5
3442
Generated 2485 of the 2485 1-4 parameter combinations
3443
Excluding 3 bonded neighbours molecule type 'nonanol'
3444
turning H bonds into constraints...
3445
Excluding 2 bonded neighbours molecule type 'SOL'
3446
turning H bonds into constraints...
3447
Removing all charge groups because cutoff-scheme=Verlet
3448
Number of degrees of freedom in T-Coupling group System is 79.00
3449

    
3450
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
3451
  NVE simulation: will use the initial temperature of 293.480 K for
3452
  determining the Verlet buffer size
3453

    
3454
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
3455
Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
3456
Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
3457
Note that mdrun will redetermine rlist based on the actual pair-list setup
3458

    
3459
NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
3460
  You are using a plain Coulomb cut-off, which might produce artifacts.
3461
  You might want to consider using PME electrostatics.
3462

    
3463

    
3464
This run will generate roughly 0 Mb of data
3465

    
3466
There were 5 notes
3467
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21.tpr, VERSION 2019.1 (double precision)
3468
Can not increase nstlist because an NVE ensemble is used
3469
Using 1 MPI process
3470
Using 1 OpenMP thread 
3471

    
3472

    
3473
NOTE: Thread affinity was not set.
3474
starting mdrun '30 system in water'
3475
16 steps,      0.0 ps.
3476

    
3477
Writing final coordinates.
3478

    
3479
               Core t (s)   Wall t (s)        (%)
3480
       Time:        0.006        0.006       98.5
3481
                 (ns/day)    (hour/ns)
3482
Performance:      255.785        0.094
3483
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21.tpr, VERSION 2019.1 (double precision)
3484
Can not increase nstlist because an NVE ensemble is used
3485
Using 1 MPI process
3486
Using 1 OpenMP thread 
3487

    
3488

    
3489
NOTE: Thread affinity was not set.
3490
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_normal.trr'
3491

    
3492
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
3493

    
3494
NOTE: 13 % of the run time was spent in pair search,
3495
      you might want to increase nstlist (this has no effect on accuracy)
3496

    
3497
               Core t (s)   Wall t (s)        (%)
3498
       Time:        0.001        0.001       96.8
3499
                 (ns/day)    (hour/ns)
3500
Performance:      996.537        0.024
3501
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_normal.edr as double precision energy file
3502
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_rerun.edr as double precision energy file
3503
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
3504

    
3505
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (137 ms)
3506
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22
3507

    
3508
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp, line 42]:
3509
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
3510
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
3511
  scheme was introduced, but the group scheme was still the default. The
3512
  default is now the Verlet scheme, so you will observe different behaviour.
3513

    
3514

    
3515
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
3516
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
3517
  that with the Verlet scheme, nstlist has no effect on the accuracy of
3518
  your simulation.
3519

    
3520

    
3521
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
3522
  Setting nstcalcenergy (100) equal to nstenergy (4)
3523

    
3524
Generated 2485 of the 2485 non-bonded parameter combinations
3525
Generating 1-4 interactions: fudge = 0.5
3526
Generated 2485 of the 2485 1-4 parameter combinations
3527
Excluding 3 bonded neighbours molecule type 'nonanol'
3528
turning H bonds into constraints...
3529
Excluding 2 bonded neighbours molecule type 'SOL'
3530
turning H bonds into constraints...
3531
Removing all charge groups because cutoff-scheme=Verlet
3532
Number of degrees of freedom in T-Coupling group System is 79.00
3533
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
3534
Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
3535
Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
3536
Note that mdrun will redetermine rlist based on the actual pair-list setup
3537

    
3538
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
3539
  You are using a plain Coulomb cut-off, which might produce artifacts.
3540
  You might want to consider using PME electrostatics.
3541

    
3542

    
3543
This run will generate roughly 0 Mb of data
3544

    
3545
There were 4 notes
3546
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22.tpr, VERSION 2019.1 (double precision)
3547
Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
3548

    
3549
Using 1 MPI process
3550
Using 1 OpenMP thread 
3551

    
3552

    
3553
NOTE: Thread affinity was not set.
3554
starting mdrun '30 system in water'
3555
16 steps,      0.0 ps.
3556

    
3557
Writing final coordinates.
3558

    
3559
               Core t (s)   Wall t (s)        (%)
3560
       Time:        0.006        0.006       98.3
3561
                 (ns/day)    (hour/ns)
3562
Performance:      250.563        0.096
3563
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22.tpr, VERSION 2019.1 (double precision)
3564
Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
3565

    
3566
Using 1 MPI process
3567
Using 1 OpenMP thread 
3568

    
3569

    
3570
NOTE: Thread affinity was not set.
3571
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_normal.trr'
3572

    
3573
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
3574

    
3575
NOTE: 14 % of the run time was spent in pair search,
3576
      you might want to increase nstlist (this has no effect on accuracy)
3577

    
3578
               Core t (s)   Wall t (s)        (%)
3579
       Time:        0.001        0.002       96.8
3580
                 (ns/day)    (hour/ns)
3581
Performance:      953.357        0.025
3582
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_normal.edr as double precision energy file
3583
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_rerun.edr as double precision energy file
3584
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
3585

    
3586
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (149 ms)
3587
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23
3588

    
3589
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp, line 42]:
3590
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
3591
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
3592
  scheme was introduced, but the group scheme was still the default. The
3593
  default is now the Verlet scheme, so you will observe different behaviour.
3594

    
3595

    
3596
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
3597
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
3598
  that with the Verlet scheme, nstlist has no effect on the accuracy of
3599
  your simulation.
3600

    
3601

    
3602
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
3603
  Setting nstcalcenergy (100) equal to nstenergy (4)
3604

    
3605
Generated 2485 of the 2485 non-bonded parameter combinations
3606
Generating 1-4 interactions: fudge = 0.5
3607
Generated 2485 of the 2485 1-4 parameter combinations
3608
Excluding 3 bonded neighbours molecule type 'nonanol'
3609
turning H bonds into constraints...
3610
Excluding 2 bonded neighbours molecule type 'SOL'
3611
turning H bonds into constraints...
3612
Removing all charge groups because cutoff-scheme=Verlet
3613
Number of degrees of freedom in T-Coupling group System is 79.00
3614
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
3615
Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
3616
Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
3617
Note that mdrun will redetermine rlist based on the actual pair-list setup
3618

    
3619
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
3620
  You are using a plain Coulomb cut-off, which might produce artifacts.
3621
  You might want to consider using PME electrostatics.
3622

    
3623

    
3624
This run will generate roughly 0 Mb of data
3625

    
3626
There were 4 notes
3627
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23.tpr, VERSION 2019.1 (double precision)
3628
Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
3629

    
3630
Using 1 MPI process
3631
Using 1 OpenMP thread 
3632

    
3633

    
3634
NOTE: Thread affinity was not set.
3635
starting mdrun '30 system in water'
3636
16 steps,      0.0 ps.
3637

    
3638
Writing final coordinates.
3639

    
3640
               Core t (s)   Wall t (s)        (%)
3641
       Time:        0.006        0.006       98.5
3642
                 (ns/day)    (hour/ns)
3643
Performance:      262.399        0.091
3644
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23.tpr, VERSION 2019.1 (double precision)
3645
Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
3646

    
3647
Using 1 MPI process
3648
Using 1 OpenMP thread 
3649

    
3650

    
3651
NOTE: Thread affinity was not set.
3652
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_normal.trr'
3653

    
3654
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
3655

    
3656
NOTE: 14 % of the run time was spent in pair search,
3657
      you might want to increase nstlist (this has no effect on accuracy)
3658

    
3659
               Core t (s)   Wall t (s)        (%)
3660
       Time:        0.002        0.002       96.0
3661
                 (ns/day)    (hour/ns)
3662
Performance:      938.829        0.026
3663
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_normal.edr as double precision energy file
3664
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_rerun.edr as double precision energy file
3665
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
3666

    
3667
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (152 ms)
3668
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24
3669

    
3670
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp, line 42]:
3671
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
3672
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
3673
  scheme was introduced, but the group scheme was still the default. The
3674
  default is now the Verlet scheme, so you will observe different behaviour.
3675

    
3676

    
3677
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
3678
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
3679
  that with the Verlet scheme, nstlist has no effect on the accuracy of
3680
  your simulation.
3681

    
3682

    
3683
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
3684
  Setting nstcalcenergy (100) equal to nstenergy (4)
3685

    
3686
Generated 2485 of the 2485 non-bonded parameter combinations
3687
Generating 1-4 interactions: fudge = 0.5
3688
Generated 2485 of the 2485 1-4 parameter combinations
3689
Excluding 3 bonded neighbours molecule type 'nonanol'
3690
turning H bonds into constraints...
3691
Excluding 2 bonded neighbours molecule type 'SOL'
3692
turning H bonds into constraints...
3693
Removing all charge groups because cutoff-scheme=Verlet
3694
Number of degrees of freedom in T-Coupling group System is 79.00
3695
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
3696
Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
3697
Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
3698
Note that mdrun will redetermine rlist based on the actual pair-list setup
3699

    
3700
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
3701
  You are using a plain Coulomb cut-off, which might produce artifacts.
3702
  You might want to consider using PME electrostatics.
3703

    
3704

    
3705
This run will generate roughly 0 Mb of data
3706

    
3707
There were 4 notes
3708
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24.tpr, VERSION 2019.1 (double precision)
3709
Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
3710

    
3711
Using 1 MPI process
3712
Using 1 OpenMP thread 
3713

    
3714

    
3715
NOTE: Thread affinity was not set.
3716
starting mdrun '30 system in water'
3717
16 steps,      0.0 ps.
3718

    
3719
Writing final coordinates.
3720

    
3721
               Core t (s)   Wall t (s)        (%)
3722
       Time:        0.004        0.004       98.5
3723
                 (ns/day)    (hour/ns)
3724
Performance:      337.641        0.071
3725
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24.tpr, VERSION 2019.1 (double precision)
3726
Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
3727

    
3728
Using 1 MPI process
3729
Using 1 OpenMP thread 
3730

    
3731

    
3732
NOTE: Thread affinity was not set.
3733
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_normal.trr'
3734

    
3735
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
3736

    
3737
NOTE: 13 % of the run time was spent in pair search,
3738
      you might want to increase nstlist (this has no effect on accuracy)
3739

    
3740
               Core t (s)   Wall t (s)        (%)
3741
       Time:        0.001        0.002       96.7
3742
                 (ns/day)    (hour/ns)
3743
Performance:      952.326        0.025
3744
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_normal.edr as double precision energy file
3745
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_rerun.edr as double precision energy file
3746
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
3747

    
3748
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (144 ms)
3749
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25
3750

    
3751
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp, line 42]:
3752
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
3753
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
3754
  scheme was introduced, but the group scheme was still the default. The
3755
  default is now the Verlet scheme, so you will observe different behaviour.
3756

    
3757

    
3758
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
3759
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
3760
  that with the Verlet scheme, nstlist has no effect on the accuracy of
3761
  your simulation.
3762

    
3763

    
3764
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
3765
  Setting nstcalcenergy (100) equal to nstenergy (4)
3766

    
3767
Generated 2485 of the 2485 non-bonded parameter combinations
3768
Generating 1-4 interactions: fudge = 0.5
3769
Generated 2485 of the 2485 1-4 parameter combinations
3770
Excluding 3 bonded neighbours molecule type 'nonanol'
3771
turning H bonds into constraints...
3772
Excluding 2 bonded neighbours molecule type 'SOL'
3773
turning H bonds into constraints...
3774
Removing all charge groups because cutoff-scheme=Verlet
3775
Number of degrees of freedom in T-Coupling group System is 79.00
3776
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
3777
Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
3778
Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
3779
Note that mdrun will redetermine rlist based on the actual pair-list setup
3780

    
3781
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
3782
  You are using a plain Coulomb cut-off, which might produce artifacts.
3783
  You might want to consider using PME electrostatics.
3784

    
3785

    
3786
This run will generate roughly 0 Mb of data
3787

    
3788
There were 4 notes
3789
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25.tpr, VERSION 2019.1 (double precision)
3790
Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
3791

    
3792
Using 1 MPI process
3793
Using 1 OpenMP thread 
3794

    
3795

    
3796
NOTE: Thread affinity was not set.
3797
starting mdrun '30 system in water'
3798
16 steps,      0.0 ps.
3799

    
3800
Writing final coordinates.
3801

    
3802
               Core t (s)   Wall t (s)        (%)
3803
       Time:        0.005        0.005       98.5
3804
                 (ns/day)    (hour/ns)
3805
Performance:      290.416        0.083
3806
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25.tpr, VERSION 2019.1 (double precision)
3807
Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
3808

    
3809
Using 1 MPI process
3810
Using 1 OpenMP thread 
3811

    
3812

    
3813
NOTE: Thread affinity was not set.
3814
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_normal.trr'
3815

    
3816
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
3817

    
3818
NOTE: 13 % of the run time was spent in pair search,
3819
      you might want to increase nstlist (this has no effect on accuracy)
3820

    
3821
               Core t (s)   Wall t (s)        (%)
3822
       Time:        0.001        0.002       96.7
3823
                 (ns/day)    (hour/ns)
3824
Performance:      961.541        0.025
3825
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_normal.edr as double precision energy file
3826
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_rerun.edr as double precision energy file
3827
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
3828

    
3829
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (150 ms)
3830
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26
3831

    
3832
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp, line 42]:
3833
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
3834
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
3835
  scheme was introduced, but the group scheme was still the default. The
3836
  default is now the Verlet scheme, so you will observe different behaviour.
3837

    
3838

    
3839
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
3840
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
3841
  that with the Verlet scheme, nstlist has no effect on the accuracy of
3842
  your simulation.
3843

    
3844

    
3845
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
3846
  Setting nstcalcenergy (100) equal to nstenergy (4)
3847

    
3848
Generated 2485 of the 2485 non-bonded parameter combinations
3849
Generating 1-4 interactions: fudge = 0.5
3850
Generated 2485 of the 2485 1-4 parameter combinations
3851
Excluding 3 bonded neighbours molecule type 'nonanol'
3852
turning H bonds into constraints...
3853
Excluding 2 bonded neighbours molecule type 'SOL'
3854
turning H bonds into constraints...
3855
Removing all charge groups because cutoff-scheme=Verlet
3856
Number of degrees of freedom in T-Coupling group System is 79.00
3857
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
3858
Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
3859
Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
3860
Note that mdrun will redetermine rlist based on the actual pair-list setup
3861

    
3862
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
3863
  You are using a plain Coulomb cut-off, which might produce artifacts.
3864
  You might want to consider using PME electrostatics.
3865

    
3866

    
3867
This run will generate roughly 0 Mb of data
3868

    
3869
There were 4 notes
3870
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26.tpr, VERSION 2019.1 (double precision)
3871
Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
3872

    
3873
Using 1 MPI process
3874
Using 1 OpenMP thread 
3875

    
3876

    
3877
NOTE: Thread affinity was not set.
3878
starting mdrun '30 system in water'
3879
16 steps,      0.0 ps.
3880

    
3881
Writing final coordinates.
3882

    
3883
               Core t (s)   Wall t (s)        (%)
3884
       Time:        0.006        0.006       98.5
3885
                 (ns/day)    (hour/ns)
3886
Performance:      260.116        0.092
3887
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26.tpr, VERSION 2019.1 (double precision)
3888
Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
3889

    
3890
Using 1 MPI process
3891
Using 1 OpenMP thread 
3892

    
3893

    
3894
NOTE: Thread affinity was not set.
3895
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_normal.trr'
3896

    
3897
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
3898

    
3899
NOTE: 14 % of the run time was spent in pair search,
3900
      you might want to increase nstlist (this has no effect on accuracy)
3901

    
3902
               Core t (s)   Wall t (s)        (%)
3903
       Time:        0.001        0.002       96.7
3904
                 (ns/day)    (hour/ns)
3905
Performance:      957.060        0.025
3906
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_normal.edr as double precision energy file
3907
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_rerun.edr as double precision energy file
3908
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
3909

    
3910
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (157 ms)
3911
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27
3912

    
3913
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp, line 42]:
3914
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
3915
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
3916
  scheme was introduced, but the group scheme was still the default. The
3917
  default is now the Verlet scheme, so you will observe different behaviour.
3918

    
3919

    
3920
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
3921
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
3922
  that with the Verlet scheme, nstlist has no effect on the accuracy of
3923
  your simulation.
3924

    
3925

    
3926
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
3927
  Setting nstcalcenergy (100) equal to nstenergy (4)
3928

    
3929
Generated 2485 of the 2485 non-bonded parameter combinations
3930
Generating 1-4 interactions: fudge = 0.5
3931
Generated 2485 of the 2485 1-4 parameter combinations
3932
Excluding 3 bonded neighbours molecule type 'nonanol'
3933
turning H bonds into constraints...
3934
Excluding 2 bonded neighbours molecule type 'SOL'
3935
turning H bonds into constraints...
3936
Removing all charge groups because cutoff-scheme=Verlet
3937
Number of degrees of freedom in T-Coupling group System is 79.00
3938
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
3939
Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
3940
Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
3941
Note that mdrun will redetermine rlist based on the actual pair-list setup
3942

    
3943
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
3944
  You are using a plain Coulomb cut-off, which might produce artifacts.
3945
  You might want to consider using PME electrostatics.
3946

    
3947

    
3948
This run will generate roughly 0 Mb of data
3949

    
3950
There were 4 notes
3951
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27.tpr, VERSION 2019.1 (double precision)
3952
Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
3953

    
3954
Using 1 MPI process
3955
Using 1 OpenMP thread 
3956

    
3957

    
3958
NOTE: Thread affinity was not set.
3959
starting mdrun '30 system in water'
3960
16 steps,      0.0 ps.
3961

    
3962
Writing final coordinates.
3963

    
3964
               Core t (s)   Wall t (s)        (%)
3965
       Time:        0.005        0.006       98.5
3966
                 (ns/day)    (hour/ns)
3967
Performance:      265.291        0.090
3968
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27.tpr, VERSION 2019.1 (double precision)
3969
Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
3970

    
3971
Using 1 MPI process
3972
Using 1 OpenMP thread 
3973

    
3974

    
3975
NOTE: Thread affinity was not set.
3976
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_normal.trr'
3977

    
3978
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
3979

    
3980
NOTE: 14 % of the run time was spent in pair search,
3981
      you might want to increase nstlist (this has no effect on accuracy)
3982

    
3983
               Core t (s)   Wall t (s)        (%)
3984
       Time:        0.001        0.002       96.7
3985
                 (ns/day)    (hour/ns)
3986
Performance:      952.620        0.025
3987
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_normal.edr as double precision energy file
3988
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_rerun.edr as double precision energy file
3989
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
3990

    
3991
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (150 ms)
3992
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28
3993

    
3994
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp, line 42]:
3995
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
3996
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
3997
  scheme was introduced, but the group scheme was still the default. The
3998
  default is now the Verlet scheme, so you will observe different behaviour.
3999

    
4000

    
4001
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
4002
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
4003
  that with the Verlet scheme, nstlist has no effect on the accuracy of
4004
  your simulation.
4005

    
4006

    
4007
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
4008
  Setting nstcalcenergy (100) equal to nstenergy (4)
4009

    
4010
Generated 2485 of the 2485 non-bonded parameter combinations
4011
Generating 1-4 interactions: fudge = 0.5
4012
Generated 2485 of the 2485 1-4 parameter combinations
4013
Excluding 3 bonded neighbours molecule type 'nonanol'
4014
turning H bonds into constraints...
4015
Excluding 2 bonded neighbours molecule type 'SOL'
4016
turning H bonds into constraints...
4017
Removing all charge groups because cutoff-scheme=Verlet
4018
Number of degrees of freedom in T-Coupling group System is 79.00
4019
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
4020
Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
4021
Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
4022
Note that mdrun will redetermine rlist based on the actual pair-list setup
4023

    
4024
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
4025
  You are using a plain Coulomb cut-off, which might produce artifacts.
4026
  You might want to consider using PME electrostatics.
4027

    
4028

    
4029
This run will generate roughly 0 Mb of data
4030

    
4031
There were 4 notes
4032
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28.tpr, VERSION 2019.1 (double precision)
4033
Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
4034

    
4035
Using 1 MPI process
4036
Using 1 OpenMP thread 
4037

    
4038

    
4039
NOTE: Thread affinity was not set.
4040
starting mdrun '30 system in water'
4041
16 steps,      0.0 ps.
4042

    
4043
Writing final coordinates.
4044

    
4045
               Core t (s)   Wall t (s)        (%)
4046
       Time:        0.005        0.005       98.6
4047
                 (ns/day)    (hour/ns)
4048
Performance:      297.039        0.081
4049
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28.tpr, VERSION 2019.1 (double precision)
4050
Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
4051

    
4052
Using 1 MPI process
4053
Using 1 OpenMP thread 
4054

    
4055

    
4056
NOTE: Thread affinity was not set.
4057
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_normal.trr'
4058

    
4059
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
4060

    
4061
NOTE: 13 % of the run time was spent in pair search,
4062
      you might want to increase nstlist (this has no effect on accuracy)
4063

    
4064
               Core t (s)   Wall t (s)        (%)
4065
       Time:        0.001        0.002       96.6
4066
                 (ns/day)    (hour/ns)
4067
Performance:      957.060        0.025
4068
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_normal.edr as double precision energy file
4069
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_rerun.edr as double precision energy file
4070
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
4071

    
4072
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (145 ms)
4073
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29
4074

    
4075
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp, line 42]:
4076
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
4077
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
4078
  scheme was introduced, but the group scheme was still the default. The
4079
  default is now the Verlet scheme, so you will observe different behaviour.
4080

    
4081

    
4082
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
4083
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
4084
  that with the Verlet scheme, nstlist has no effect on the accuracy of
4085
  your simulation.
4086

    
4087

    
4088
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
4089
  Setting nstcalcenergy (100) equal to nstenergy (4)
4090

    
4091
Generated 2485 of the 2485 non-bonded parameter combinations
4092
Generating 1-4 interactions: fudge = 0.5
4093
Generated 2485 of the 2485 1-4 parameter combinations
4094
Excluding 3 bonded neighbours molecule type 'nonanol'
4095
turning H bonds into constraints...
4096
Excluding 2 bonded neighbours molecule type 'SOL'
4097
turning H bonds into constraints...
4098
Removing all charge groups because cutoff-scheme=Verlet
4099
Number of degrees of freedom in T-Coupling group System is 79.00
4100
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
4101
Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
4102
Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
4103
Note that mdrun will redetermine rlist based on the actual pair-list setup
4104

    
4105
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
4106
  You are using a plain Coulomb cut-off, which might produce artifacts.
4107
  You might want to consider using PME electrostatics.
4108

    
4109

    
4110
This run will generate roughly 0 Mb of data
4111

    
4112
There were 4 notes
4113
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29.tpr, VERSION 2019.1 (double precision)
4114
Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
4115

    
4116
Using 1 MPI process
4117
Using 1 OpenMP thread 
4118

    
4119

    
4120
NOTE: Thread affinity was not set.
4121
starting mdrun '30 system in water'
4122
16 steps,      0.0 ps.
4123

    
4124
Writing final coordinates.
4125

    
4126
               Core t (s)   Wall t (s)        (%)
4127
       Time:        0.005        0.005       98.4
4128
                 (ns/day)    (hour/ns)
4129
Performance:      278.646        0.086
4130
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29.tpr, VERSION 2019.1 (double precision)
4131
Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
4132

    
4133
Using 1 MPI process
4134
Using 1 OpenMP thread 
4135

    
4136

    
4137
NOTE: Thread affinity was not set.
4138
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_normal.trr'
4139

    
4140
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
4141

    
4142
NOTE: 14 % of the run time was spent in pair search,
4143
      you might want to increase nstlist (this has no effect on accuracy)
4144

    
4145
               Core t (s)   Wall t (s)        (%)
4146
       Time:        0.001        0.001       96.7
4147
                 (ns/day)    (hour/ns)
4148
Performance:     1136.222        0.021
4149
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_normal.edr as double precision energy file
4150
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_rerun.edr as double precision energy file
4151
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
4152

    
4153
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (145 ms)
4154
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30
4155

    
4156
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp, line 42]:
4157
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
4158
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
4159
  scheme was introduced, but the group scheme was still the default. The
4160
  default is now the Verlet scheme, so you will observe different behaviour.
4161

    
4162

    
4163
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
4164
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
4165
  that with the Verlet scheme, nstlist has no effect on the accuracy of
4166
  your simulation.
4167

    
4168

    
4169
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
4170
  Setting nstcalcenergy (100) equal to nstenergy (4)
4171

    
4172
Generated 2485 of the 2485 non-bonded parameter combinations
4173
Generating 1-4 interactions: fudge = 0.5
4174
Generated 2485 of the 2485 1-4 parameter combinations
4175
Excluding 3 bonded neighbours molecule type 'nonanol'
4176
turning H bonds into constraints...
4177
Excluding 2 bonded neighbours molecule type 'SOL'
4178
turning H bonds into constraints...
4179
Removing all charge groups because cutoff-scheme=Verlet
4180
Number of degrees of freedom in T-Coupling group System is 79.00
4181
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
4182
Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
4183
Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
4184
Note that mdrun will redetermine rlist based on the actual pair-list setup
4185

    
4186
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
4187
  You are using a plain Coulomb cut-off, which might produce artifacts.
4188
  You might want to consider using PME electrostatics.
4189

    
4190

    
4191
This run will generate roughly 0 Mb of data
4192

    
4193
There were 4 notes
4194
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30.tpr, VERSION 2019.1 (double precision)
4195
Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
4196

    
4197
Using 1 MPI process
4198
Using 1 OpenMP thread 
4199

    
4200

    
4201
NOTE: Thread affinity was not set.
4202
starting mdrun '30 system in water'
4203
16 steps,      0.0 ps.
4204

    
4205
Writing final coordinates.
4206

    
4207
               Core t (s)   Wall t (s)        (%)
4208
       Time:        0.005        0.006       98.5
4209
                 (ns/day)    (hour/ns)
4210
Performance:      264.528        0.091
4211
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30.tpr, VERSION 2019.1 (double precision)
4212
Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
4213

    
4214
Using 1 MPI process
4215
Using 1 OpenMP thread 
4216

    
4217

    
4218
NOTE: Thread affinity was not set.
4219
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_normal.trr'
4220

    
4221
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
4222

    
4223
NOTE: 13 % of the run time was spent in pair search,
4224
      you might want to increase nstlist (this has no effect on accuracy)
4225

    
4226
               Core t (s)   Wall t (s)        (%)
4227
       Time:        0.001        0.001       96.7
4228
                 (ns/day)    (hour/ns)
4229
Performance:     1026.252        0.023
4230
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_normal.edr as double precision energy file
4231
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_rerun.edr as double precision energy file
4232
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
4233

    
4234
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (149 ms)
4235
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31
4236

    
4237
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp, line 42]:
4238
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
4239
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
4240
  scheme was introduced, but the group scheme was still the default. The
4241
  default is now the Verlet scheme, so you will observe different behaviour.
4242

    
4243

    
4244
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
4245
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
4246
  that with the Verlet scheme, nstlist has no effect on the accuracy of
4247
  your simulation.
4248

    
4249

    
4250
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
4251
  Setting nstcalcenergy (100) equal to nstenergy (4)
4252

    
4253
Generated 2485 of the 2485 non-bonded parameter combinations
4254
Generating 1-4 interactions: fudge = 0.5
4255
Generated 2485 of the 2485 1-4 parameter combinations
4256
Excluding 3 bonded neighbours molecule type 'nonanol'
4257
turning H bonds into constraints...
4258
Excluding 2 bonded neighbours molecule type 'SOL'
4259
turning H bonds into constraints...
4260
Removing all charge groups because cutoff-scheme=Verlet
4261
Number of degrees of freedom in T-Coupling group System is 79.00
4262
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
4263
Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
4264
Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
4265
Note that mdrun will redetermine rlist based on the actual pair-list setup
4266

    
4267
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
4268
  You are using a plain Coulomb cut-off, which might produce artifacts.
4269
  You might want to consider using PME electrostatics.
4270

    
4271

    
4272
This run will generate roughly 0 Mb of data
4273

    
4274
There were 4 notes
4275
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31.tpr, VERSION 2019.1 (double precision)
4276
Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
4277

    
4278
Using 1 MPI process
4279
Using 1 OpenMP thread 
4280

    
4281

    
4282
NOTE: Thread affinity was not set.
4283
starting mdrun '30 system in water'
4284
16 steps,      0.0 ps.
4285

    
4286
Writing final coordinates.
4287

    
4288
               Core t (s)   Wall t (s)        (%)
4289
       Time:        0.005        0.005       98.5
4290
                 (ns/day)    (hour/ns)
4291
Performance:      270.795        0.089
4292
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31.tpr, VERSION 2019.1 (double precision)
4293
Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
4294

    
4295
Using 1 MPI process
4296
Using 1 OpenMP thread 
4297

    
4298

    
4299
NOTE: Thread affinity was not set.
4300
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_normal.trr'
4301

    
4302
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
4303

    
4304
NOTE: 13 % of the run time was spent in pair search,
4305
      you might want to increase nstlist (this has no effect on accuracy)
4306

    
4307
               Core t (s)   Wall t (s)        (%)
4308
       Time:        0.001        0.002       96.7
4309
                 (ns/day)    (hour/ns)
4310
Performance:      954.243        0.025
4311
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_normal.edr as double precision energy file
4312
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_rerun.edr as double precision energy file
4313
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
4314

    
4315
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (150 ms)
4316
[ RUN      ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32
4317

    
4318
NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp, line 42]:
4319
  /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
4320
  was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
4321
  scheme was introduced, but the group scheme was still the default. The
4322
  default is now the Verlet scheme, so you will observe different behaviour.
4323

    
4324

    
4325
NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
4326
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
4327
  that with the Verlet scheme, nstlist has no effect on the accuracy of
4328
  your simulation.
4329

    
4330

    
4331
NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
4332
  Setting nstcalcenergy (100) equal to nstenergy (4)
4333

    
4334
Generated 2485 of the 2485 non-bonded parameter combinations
4335
Generating 1-4 interactions: fudge = 0.5
4336
Generated 2485 of the 2485 1-4 parameter combinations
4337
Excluding 3 bonded neighbours molecule type 'nonanol'
4338
turning H bonds into constraints...
4339
Excluding 2 bonded neighbours molecule type 'SOL'
4340
turning H bonds into constraints...
4341
Removing all charge groups because cutoff-scheme=Verlet
4342
Number of degrees of freedom in T-Coupling group System is 79.00
4343
Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
4344
Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
4345
Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
4346
Note that mdrun will redetermine rlist based on the actual pair-list setup
4347

    
4348
NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
4349
  You are using a plain Coulomb cut-off, which might produce artifacts.
4350
  You might want to consider using PME electrostatics.
4351

    
4352

    
4353
This run will generate roughly 0 Mb of data
4354

    
4355
There were 4 notes
4356
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32.tpr, VERSION 2019.1 (double precision)
4357
Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
4358

    
4359
Using 1 MPI process
4360
Using 1 OpenMP thread 
4361

    
4362

    
4363
NOTE: Thread affinity was not set.
4364
starting mdrun '30 system in water'
4365
16 steps,      0.0 ps.
4366

    
4367
Writing final coordinates.
4368

    
4369
               Core t (s)   Wall t (s)        (%)
4370
       Time:        0.005        0.006       98.5
4371
                 (ns/day)    (hour/ns)
4372
Performance:      266.681        0.090
4373
Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32.tpr, VERSION 2019.1 (double precision)
4374
Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
4375

    
4376
Using 1 MPI process
4377
Using 1 OpenMP thread 
4378

    
4379

    
4380
NOTE: Thread affinity was not set.
4381
starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_normal.trr'
4382

    
4383
Reading frame       0 time    0.000   
Reading frame       1 time    0.004   
Reading frame       2 time    0.008   
Reading frame       3 time    0.012   
Reading frame       4 time    0.016   
Last frame          4 time    0.016   
4384

    
4385
NOTE: 13 % of the run time was spent in pair search,
4386
      you might want to increase nstlist (this has no effect on accuracy)
4387

    
4388
               Core t (s)   Wall t (s)        (%)
4389
       Time:        0.001        0.002       96.7
4390
                 (ns/day)    (hour/ns)
4391
Performance:      960.342        0.025
4392
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_normal.edr as double precision energy file
4393
Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_rerun.edr as double precision energy file
4394
Reading energy frame      0 time    0.000         
Reading energy frame      0 time    0.000         
Reading energy frame      1 time    0.004         
Reading energy frame      1 time    0.004         
Reading energy frame      2 time    0.008         
Reading energy frame      2 time    0.008         
Reading energy frame      3 time    0.012         
Reading energy frame      3 time    0.012         
Reading energy frame      4 time    0.016         
Reading energy frame      4 time    0.016         
Last energy frame read 4 time    0.016         
Last energy frame read 4 time    0.016         
4395

    
4396
[       OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (152 ms)
4397
[----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (4613 ms total)
4398

    
4399
[----------] Global test environment tear-down
4400
[==========] 57 tests from 4 test cases ran. (8061 ms total)
4401
[  PASSED  ] 56 tests.
4402
[  FAILED  ] 1 test, listed below:
4403
[  FAILED  ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5, where GetParam() = ("glycine_no_constraints_vacuo", "l-bfgs")
4404

    
4405
 1 FAILED TEST