Project

General

Profile

PME.log

Output with PME - Igor Leontyev, 07/24/2014 12:31 AM

 
1
Log file opened on Wed Jul 23 15:10:37 2014
2
Host: compute-0-1.local  pid: 13596  rank ID: 0  number of ranks:  1
3
GROMACS:    gmx mdrun, VERSION 5.0 (double precision)
4

    
5
GROMACS is written by:
6
Emile Apol         Rossen Apostolov   Herman J.C. Berendsen Par Bjelkmar       
7
Aldert van Buuren  Rudi van Drunen    Anton Feenstra     Sebastian Fritsch  
8
Gerrit Groenhof    Christoph Junghans Peter Kasson       Carsten Kutzner    
9
Per Larsson        Justin A. Lemkul   Magnus Lundborg    Pieter Meulenhoff  
10
Erik Marklund      Teemu Murtola      Szilard Pall       Sander Pronk       
11
Roland Schulz      Alexey Shvetsov    Michael Shirts     Alfons Sijbers     
12
Peter Tieleman     Christian Wennberg Maarten Wolf       
13
and the project leaders:
14
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
15

    
16
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
17
Copyright (c) 2001-2014, The GROMACS development team at
18
Uppsala University, Stockholm University and
19
the Royal Institute of Technology, Sweden.
20
check out http://www.gromacs.org for more information.
21

    
22
GROMACS is free software; you can redistribute it and/or modify it
23
under the terms of the GNU Lesser General Public License
24
as published by the Free Software Foundation; either version 2.1
25
of the License, or (at your option) any later version.
26

    
27
GROMACS:      gmx mdrun, VERSION 5.0 (double precision)
28
Executable:   /home/leontyev/programs/bin/gromacs/gromacs-5.0/bin/gmx_d
29
Library dir:  /home/leontyev/programs/bin/gromacs/gromacs-5.0/share/gromacs/top
30
Command line:
31
  mdrun_d -nt 1 -s Methylacetamide.tpr -o Methylacetamide.trr -x Methylacetamide.xtc -c Methylacetamide_fin.gro -g Methylacetamide.log
32

    
33
Gromacs version:    VERSION 5.0
34
Precision:          double
35
Memory model:       64 bit
36
MPI library:        thread_mpi
37
OpenMP support:     enabled
38
GPU support:        disabled
39
invsqrt routine:    gmx_software_invsqrt(x)
40
SIMD instructions:  AVX_256
41
FFT library:        fftw-3.3.4-sse2-avx
42
RDTSCP usage:       enabled
43
C++11 compilation:  enabled
44
TNG support:        enabled
45
Tracing support:    disabled
46
Built on:           Fri Jul 18 22:55:04 PDT 2014
47
Built by:           leontyev@cluster01.interxinc.com [CMAKE]
48
Build OS/arch:      Linux 2.6.32-431.el6.x86_64 x86_64
49
Build CPU vendor:   GenuineIntel
50
Build CPU brand:    Intel(R) Xeon(R) CPU E5-1620 0 @ 3.60GHz
51
Build CPU family:   6   Model: 45   Stepping: 7
52
Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
53
C compiler:         /export/apps/gcc/4.8.2/bin/gcc-gcc-4.8 GNU 4.8.2
54
C compiler flags:    -mavx   -Wno-maybe-uninitialized -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter  -static-libgcc -static-libstdc++  -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  -Wno-array-bounds  -O3 -DNDEBUG
55
C++ compiler:       /export/apps/gcc/4.8.2/bin/g++-gcc-4.8 GNU 4.8.2
56
C++ compiler flags:  -mavx   -std=c++0x -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function   -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  -Wno-array-bounds  -O3 -DNDEBUG
57
Boost version:      1.55.0 (internal)
58

    
59

    
60

    
61
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
62
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
63
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
64
molecular simulation
65
J. Chem. Theory Comput. 4 (2008) pp. 435-447
66
-------- -------- --- Thank You --- -------- --------
67

    
68

    
69
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
70
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
71
Berendsen
72
GROMACS: Fast, Flexible and Free
73
J. Comp. Chem. 26 (2005) pp. 1701-1719
74
-------- -------- --- Thank You --- -------- --------
75

    
76

    
77
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
78
E. Lindahl and B. Hess and D. van der Spoel
79
GROMACS 3.0: A package for molecular simulation and trajectory analysis
80
J. Mol. Mod. 7 (2001) pp. 306-317
81
-------- -------- --- Thank You --- -------- --------
82

    
83

    
84
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
85
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
86
GROMACS: A message-passing parallel molecular dynamics implementation
87
Comp. Phys. Comm. 91 (1995) pp. 43-56
88
-------- -------- --- Thank You --- -------- --------
89

    
90
Input Parameters:
91
   integrator                     = md
92
   tinit                          = 0
93
   dt                             = 0.001
94
   nsteps                         = 10
95
   init-step                      = 0
96
   simulation-part                = 1
97
   comm-mode                      = Linear
98
   nstcomm                        = 103
99
   bd-fric                        = 0
100
   ld-seed                        = 4079259596
101
   emtol                          = 10
102
   emstep                         = 0.01
103
   niter                          = 20
104
   fcstep                         = 0
105
   nstcgsteep                     = 1000
106
   nbfgscorr                      = 10
107
   rtpi                           = 0.05
108
   nstxout                        = 10000000
109
   nstvout                        = 10000000
110
   nstfout                        = 0
111
   nstlog                         = 1
112
   nstcalcenergy                  = 100
113
   nstenergy                      = 100
114
   nstxout-compressed             = 0
115
   compressed-x-precision         = 1000
116
   cutoff-scheme                  = Group
117
   nstlist                        = 5
118
   ns-type                        = Grid
119
   pbc                            = xyz
120
   periodic-molecules             = FALSE
121
   verlet-buffer-tolerance        = 0.005
122
   rlist                          = 1.3
123
   rlistlong                      = 1.3
124
   nstcalclr                      = 0
125
   coulombtype                    = PME
126
   coulomb-modifier               = None
127
   rcoulomb-switch                = 1.2
128
   rcoulomb                       = 1.3
129
   epsilon-r                      = 1
130
   epsilon-rf                     = inf
131
   vdw-type                       = Cut-off
132
   vdw-modifier                   = None
133
   rvdw-switch                    = 0
134
   rvdw                           = 1.3
135
   DispCorr                       = EnerPres
136
   table-extension                = 1
137
   fourierspacing                 = 0.12
138
   fourier-nx                     = 28
139
   fourier-ny                     = 28
140
   fourier-nz                     = 28
141
   pme-order                      = 4
142
   ewald-rtol                     = 1e-05
143
   ewald-rtol-lj                  = 0.001
144
   lj-pme-comb-rule               = Geometric
145
   ewald-geometry                 = 0
146
   epsilon-surface                = 0
147
   implicit-solvent               = No
148
   gb-algorithm                   = Still
149
   nstgbradii                     = 1
150
   rgbradii                       = 1
151
   gb-epsilon-solvent             = 80
152
   gb-saltconc                    = 0
153
   gb-obc-alpha                   = 1
154
   gb-obc-beta                    = 0.8
155
   gb-obc-gamma                   = 4.85
156
   gb-dielectric-offset           = 0.009
157
   sa-algorithm                   = Ace-approximation
158
   sa-surface-tension             = 2.05016
159
   tcoupl                         = Nose-Hoover
160
   nsttcouple                     = 5
161
   nh-chain-length                = 1
162
   print-nose-hoover-chain-variables = FALSE
163
   pcoupl                         = Berendsen
164
   pcoupltype                     = Isotropic
165
   nstpcouple                     = 5
166
   tau-p                          = 5
167
   compressibility (3x3):
168
      compressibility[    0]={ 4.50000e-05,  0.00000e+00,  0.00000e+00}
169
      compressibility[    1]={ 0.00000e+00,  4.50000e-05,  0.00000e+00}
170
      compressibility[    2]={ 0.00000e+00,  0.00000e+00,  4.50000e-05}
171
   ref-p (3x3):
172
      ref-p[    0]={ 1.01325e+00,  0.00000e+00,  0.00000e+00}
173
      ref-p[    1]={ 0.00000e+00,  1.01325e+00,  0.00000e+00}
174
      ref-p[    2]={ 0.00000e+00,  0.00000e+00,  1.01325e+00}
175
   refcoord-scaling               = No
176
   posres-com (3):
177
      posres-com[0]= 0.00000e+00
178
      posres-com[1]= 0.00000e+00
179
      posres-com[2]= 0.00000e+00
180
   posres-comB (3):
181
      posres-comB[0]= 0.00000e+00
182
      posres-comB[1]= 0.00000e+00
183
      posres-comB[2]= 0.00000e+00
184
   QMMM                           = FALSE
185
   QMconstraints                  = 0
186
   QMMMscheme                     = 0
187
   MMChargeScaleFactor            = 1
188
qm-opts:
189
   ngQM                           = 0
190
   constraint-algorithm           = Lincs
191
   continuation                   = FALSE
192
   Shake-SOR                      = FALSE
193
   shake-tol                      = 0.0001
194
   lincs-order                    = 4
195
   lincs-iter                     = 1
196
   lincs-warnangle                = 30
197
   nwall                          = 0
198
   wall-type                      = 9-3
199
   wall-r-linpot                  = -1
200
   wall-atomtype[0]               = -1
201
   wall-atomtype[1]               = -1
202
   wall-density[0]                = 0
203
   wall-density[1]                = 0
204
   wall-ewald-zfac                = 3
205
   pull                           = no
206
   rotation                       = FALSE
207
   interactiveMD                  = FALSE
208
   disre                          = No
209
   disre-weighting                = Conservative
210
   disre-mixed                    = FALSE
211
   dr-fc                          = 1000
212
   dr-tau                         = 0
213
   nstdisreout                    = 100
214
   orire-fc                       = 0
215
   orire-tau                      = 0
216
   nstorireout                    = 100
217
   free-energy                    = no
218
   cos-acceleration               = 0
219
   deform (3x3):
220
      deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
221
      deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
222
      deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
223
   simulated-tempering            = FALSE
224
   E-x:
225
      n = 0
226
   E-xt:
227
      n = 0
228
   E-y:
229
      n = 0
230
   E-yt:
231
      n = 0
232
   E-z:
233
      n = 0
234
   E-zt:
235
      n = 0
236
   swapcoords                     = no
237
   adress                         = FALSE
238
   userint1                       = 0
239
   userint2                       = 0
240
   userint3                       = 0
241
   userint4                       = 0
242
   userreal1                      = 0
243
   userreal2                      = 0
244
   userreal3                      = 0
245
   userreal4                      = 0
246
grpopts:
247
   nrdf:        7125
248
   ref-t:      298.15
249
   tau-t:           1
250
annealing:          No
251
annealing-npoints:           0
252
   acc:	           0           0           0
253
   nfreeze:           N           N           N
254
   energygrp-flags[  0]: 0
255
Using 1 MPI thread
256

    
257
Detecting CPU SIMD instructions.
258
Present hardware specification:
259
Vendor: GenuineIntel
260
Brand:  Intel(R) Xeon(R) CPU E5-2665 0 @ 2.40GHz
261
Family:  6  Model: 45  Stepping:  7
262
Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
263
SIMD instructions most likely to fit this hardware: AVX_256
264
SIMD instructions selected at GROMACS compile time: AVX_256
265

    
266

    
267
NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be
268
removed in a future release when 'verlet' supports all interaction forms.
269

    
270
Table routines are used for coulomb: FALSE
271
Table routines are used for vdw:     FALSE
272
Will do PME sum in reciprocal space for electrostatic interactions.
273

    
274
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
275
U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
276
A smooth particle mesh Ewald method
277
J. Chem. Phys. 103 (1995) pp. 8577-8592
278
-------- -------- --- Thank You --- -------- --------
279

    
280
Will do ordinary reciprocal space Ewald sum.
281
Using a Gaussian width (1/beta) of 0.416211 nm for Ewald
282
Cut-off's:   NS: 1.3   Coulomb: 1.3   LJ: 1.3
283
Long Range LJ corr.: <C6> 7.6923e-04
284
System total charge: -0.000
285
Generated table with 4600 data points for Ewald.
286
Tabscale = 2000 points/nm
287
Generated table with 4600 data points for LJ6.
288
Tabscale = 2000 points/nm
289
Generated table with 4600 data points for LJ12.
290
Tabscale = 2000 points/nm
291
Generated table with 4600 data points for 1-4 COUL.
292
Tabscale = 2000 points/nm
293
Generated table with 4600 data points for 1-4 LJ6.
294
Tabscale = 2000 points/nm
295
Generated table with 4600 data points for 1-4 LJ12.
296
Tabscale = 2000 points/nm
297
Potential shift: LJ r^-12: 0.000e+00 r^-6: 0.000e+00, Ewald -0.000e+00
298
Initialized non-bonded Ewald correction tables, spacing: 1.06e-03 size: 2164
299

    
300
Removing pbc first time
301
Center of mass motion removal mode is Linear
302
We have the following groups for center of mass motion removal:
303
  0:  rest
304
There are: 2376 Atoms
305
Max number of connections per atom is 34
306
Total number of connections is 35640
307
Max number of graph edges per atom is 4
308
Total number of graph edges is 4356
309
Initial temperature: 294.781 K
310

    
311
Started mdrun on rank 0 Wed Jul 23 15:10:37 2014
312
           Step           Time         Lambda
313
              0        0.00000        0.00000
314

    
315

    
316
Grid: 3 x 3 x 3 cells
317
   Energies (kJ/mol)
318
           Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
319
    2.34312e+03    5.14151e+03    1.33092e+02    3.55685e+03    8.34370e+02
320
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
321
   -1.29147e+04   -3.28852e+03   -1.28735e+02   -1.32510e+03   -2.21748e+03
322
      Potential    Kinetic En.   Total Energy    Temperature Pres. DC (bar)
323
   -7.86555e+03    8.77660e+03    9.11051e+02    2.96302e+02   -1.32952e+02
324
 Pressure (bar)
325
   -1.06735e+03
326

    
327
           Step           Time         Lambda
328
              1        0.00100        0.00000
329

    
330
   Energies (kJ/mol)
331
           Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
332
    2.25870e+03    5.08286e+03    1.31952e+02    3.54895e+03    8.29584e+02
333
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
334
   -1.29222e+04   -3.28496e+03   -1.28735e+02   -1.32305e+03   -2.21615e+03
335
      Potential    Kinetic En.   Total Energy    Temperature Pres. DC (bar)
336
   -8.02299e+03    8.92015e+03    8.97160e+02    3.01148e+02   -1.32952e+02
337
 Pressure (bar)
338
    1.63500e+02
339

    
340
           Step           Time         Lambda
341
              2        0.00200        0.00000
342

    
343
   Energies (kJ/mol)
344
           Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
345
    2.18768e+03    4.97970e+03    1.29586e+02    3.53166e+03    8.23951e+02
346
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
347
   -1.29347e+04   -3.28841e+03   -1.28741e+02   -1.31863e+03   -2.21457e+03
348
      Potential    Kinetic En.   Total Energy    Temperature Pres. DC (bar)
349
   -8.23246e+03    9.11937e+03    8.86912e+02    3.07874e+02   -1.32965e+02
350
 Pressure (bar)
351
    2.07711e+03
352

    
353
           Step           Time         Lambda
354
              3        0.00300        0.00000
355

    
356
   Energies (kJ/mol)
357
           Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
358
    2.18880e+03    4.84707e+03    1.26382e+02    3.50555e+03    8.18121e+02
359
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
360
   -1.29476e+04   -3.30159e+03   -1.28741e+02   -1.31679e+03   -2.21362e+03
361
      Potential    Kinetic En.   Total Energy    Temperature Pres. DC (bar)
362
   -8.42244e+03    9.31325e+03    8.90811e+02    3.14420e+02   -1.32965e+02
363
 Pressure (bar)
364
    4.01299e+03
365

    
366
           Step           Time         Lambda
367
              4        0.00400        0.00000
368

    
369
   Energies (kJ/mol)
370
           Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
371
    2.20659e+03    4.70899e+03    1.22781e+02    3.47177e+03    8.13710e+02
372
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
373
   -1.29569e+04   -3.32337e+03   -1.28741e+02   -1.32244e+03   -2.21411e+03
374
      Potential    Kinetic En.   Total Energy    Temperature Pres. DC (bar)
375
   -8.62169e+03    9.51829e+03    8.96599e+02    3.21342e+02   -1.32965e+02
376
 Pressure (bar)
377
    5.47653e+03
378

    
379
           Step           Time         Lambda
380
              5        0.00500        0.00000
381

    
382
   Energies (kJ/mol)
383
           Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
384
    2.16582e+03    4.59404e+03    1.19137e+02    3.43206e+03    8.11586e+02
385
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
386
   -1.29598e+04   -3.34981e+03   -1.28741e+02   -1.33819e+03   -2.21640e+03
387
      Potential    Kinetic En.   Total Energy    Temperature Pres. DC (bar)
388
   -8.87029e+03    9.75911e+03    8.88816e+02    3.29472e+02   -1.32965e+02
389
 Pressure (bar)
390
    6.16503e+03
391

    
392
           Step           Time         Lambda
393
              6        0.00600        0.00000
394

    
395
   Energies (kJ/mol)
396
           Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
397
    2.09465e+03    4.52640e+03    1.15626e+02    3.38857e+03    8.11954e+02
398
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
399
   -1.29565e+04   -3.37629e+03   -1.28741e+02   -1.36332e+03   -2.22027e+03
400
      Potential    Kinetic En.   Total Energy    Temperature Pres. DC (bar)
401
   -9.10795e+03    9.98096e+03    8.73005e+02    3.36962e+02   -1.32965e+02
402
 Pressure (bar)
403
    6.05073e+03
404

    
405
           Step           Time         Lambda
406
              7        0.00700        0.00000
407

    
408
   Energies (kJ/mol)
409
           Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
410
    2.09536e+03    4.51630e+03    1.12242e+02    3.34337e+03    8.12749e+02
411
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
412
   -1.29487e+04   -3.40256e+03   -1.28706e+02   -1.39359e+03   -2.22488e+03
413
      Potential    Kinetic En.   Total Energy    Temperature Pres. DC (bar)
414
   -9.21845e+03    1.00881e+04    8.69608e+02    3.40578e+02   -1.32891e+02
415
 Pressure (bar)
416
    5.22124e+03
417

    
418
           Step           Time         Lambda
419
              8        0.00800        0.00000
420

    
421
   Energies (kJ/mol)
422
           Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
423
    2.18729e+03    4.55616e+03    1.08875e+02    3.29815e+03    8.16690e+02
424
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
425
   -1.29436e+04   -3.42482e+03   -1.28706e+02   -1.42328e+03   -2.22920e+03
426
      Potential    Kinetic En.   Total Energy    Temperature Pres. DC (bar)
427
   -9.18240e+03    1.00699e+04    8.87536e+02    3.39966e+02   -1.32891e+02
428
 Pressure (bar)
429
    4.56883e+03
430

    
431
           Step           Time         Lambda
432
              9        0.00900        0.00000
433

    
434
   Energies (kJ/mol)
435
           Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
436
    2.26212e+03    4.62521e+03    1.05429e+02    3.25408e+03    8.21330e+02
437
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
438
   -1.29445e+04   -3.44812e+03   -1.28706e+02   -1.44546e+03   -2.23212e+03
439
      Potential    Kinetic En.   Total Energy    Temperature Pres. DC (bar)
440
   -9.13067e+03    1.00356e+04    9.04910e+02    3.38806e+02   -1.32891e+02
441
 Pressure (bar)
442
    4.49459e+03
443

    
444
           Step           Time         Lambda
445
             10        0.01000        0.00000
446

    
447
Writing checkpoint, step 10 at Wed Jul 23 15:10:37 2014
448

    
449

    
450
   Energies (kJ/mol)
451
           Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
452
    2.21648e+03    4.69922e+03    1.01927e+02    3.21190e+03    8.26075e+02
453
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
454
   -1.29541e+04   -3.47543e+03   -1.28706e+02   -1.45550e+03   -2.23304e+03
455
      Potential    Kinetic En.   Total Energy    Temperature Pres. DC (bar)
456
   -9.19120e+03    1.00913e+04    9.00066e+02    3.40686e+02   -1.32891e+02
457
 Pressure (bar)
458
    5.34039e+03
459

    
460
	<======  ###############  ==>
461
	<====  A V E R A G E S  ====>
462
	<==  ###############  ======>
463

    
464
	Statistics over 11 steps using 11 frames
465

    
466
   Energies (kJ/mol)
467
           Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
468
    2.20060e+03    4.75250e+03    1.18821e+02    3.41299e+03    8.20011e+02
469
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
470
   -1.29439e+04   -3.36035e+03   -1.28727e+02   -1.36594e+03   -2.22108e+03
471
      Potential    Kinetic En.   Total Energy    Temperature Pres. DC (bar)
472
   -8.71510e+03    9.60660e+03    8.91498e+02    3.24323e+02   -1.32936e+02
473
 Pressure (bar)
474
    3.86396e+03
475

    
476
          Box-X          Box-Y          Box-Z
477
    3.18007e+00    3.18007e+00    3.18007e+00
478

    
479
   Total Virial (kJ/mol)
480
   -6.14293e+02   -2.49406e+02   -2.10495e+02
481
   -2.49406e+02   -7.39892e+02   -5.44235e+02
482
   -2.10495e+02   -5.44235e+02   -2.64323e+02
483

    
484
   Pressure (bar)
485
    4.06644e+03    3.07847e+02    3.03916e+02
486
    3.07847e+02    3.96556e+03    4.76728e+02
487
    3.03916e+02    4.76728e+02    3.55988e+03
488

    
489

    
490
	M E G A - F L O P S   A C C O U N T I N G
491

    
492
 NB=Group-cutoff nonbonded kernels    NxN=N-by-N cluster Verlet kernels
493
 RF=Reaction-Field  VdW=Van der Waals  QSTab=quadratic-spline table
494
 W3=SPC/TIP3p  W4=TIP4p (single or pairs)
495
 V&F=Potential and force  V=Potential only  F=Force only
496

    
497
 Computing:                               M-Number         M-Flops  % Flops
498
-----------------------------------------------------------------------------
499
 NB Elec. [V&F]                          66.822288          66.822    11.6
500
 NB VdW & Elec. [V&F]                   416.214936         416.215    72.4
501
 1,4 nonbonded interactions               0.034848           3.136     0.5
502
 Calc Weights                             0.078408           2.823     0.5
503
 Spread Q Bspline                         1.672704           3.345     0.6
504
 Gather F Bspline                         1.672704          10.036     1.7
505
 3D-FFT                                   6.965046          55.720     9.7
506
 Solve PME                                0.008624           0.552     0.1
507
 NS-Pairs                                 0.066219           1.391     0.2
508
 Reset In Box                             0.000594           0.002     0.0
509
 Shift-X                                  0.052272           0.314     0.1
510
 CG-CoM                                   0.007128           0.021     0.0
511
 Bonds                                    0.023958           1.414     0.2
512
 Angles                                   0.039204           6.586     1.1
513
 Propers                                  0.004356           0.998     0.2
514
 RB-Dihedrals                             0.015246           3.766     0.7
515
 Virial                                   0.026631           0.479     0.1
516
 Stop-CM                                  0.004752           0.048     0.0
517
 P-Coupling                               0.026136           0.157     0.0
518
 Calc-Ekin                                0.028512           0.770     0.1
519
-----------------------------------------------------------------------------
520
 Total                                                     574.594   100.0
521
-----------------------------------------------------------------------------
522

    
523

    
524
     R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
525

    
526
On 1 MPI rank
527

    
528
 Computing:          Num   Num      Call    Wall time         Giga-Cycles
529
                     Ranks Threads  Count      (s)         total sum    %
530
-----------------------------------------------------------------------------
531
 Neighbor search        1    1          3       0.018          0.043   8.2
532
 Force                  1    1         11       0.167          0.402  76.4
533
 PME mesh               1    1         11       0.012          0.029   5.5
534
 Write traj.            1    1          2       0.020          0.047   9.0
535
 Update                 1    1         11       0.001          0.002   0.3
536
 Rest                                           0.001          0.003   0.6
537
-----------------------------------------------------------------------------
538
 Total                                          0.219          0.526 100.0
539
-----------------------------------------------------------------------------
540
 Breakdown of PME mesh computation
541
-----------------------------------------------------------------------------
542
 PME spread/gather      1    1         22       0.005          0.012   2.3
543
 PME 3D-FFT             1    1         22       0.004          0.009   1.7
544
 PME solve Elec         1    1         11       0.003          0.008   1.4
545
-----------------------------------------------------------------------------
546

    
547
               Core t (s)   Wall t (s)        (%)
548
       Time:        0.207        0.219       94.8
549
                 (ns/day)    (hour/ns)
550
Performance:        4.344        5.525
551
Finished mdrun on rank 0 Wed Jul 23 15:10:37 2014