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md.log

Magnus Lundborg, 02/02/2018 02:22 PM

 
1
Log file opened on Fri Feb  2 10:56:31 2018
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Host: erco-gpu17  pid: 8821  rank ID: 0  number of ranks:  1
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                       :-) GROMACS - gmx mdrun, 2018 (-:
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                            GROMACS is written by:
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     Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par Bjelkmar   
7
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra    Gerrit Groenhof  
8
 Christoph Junghans   Anca Hamuraru    Vincent Hindriksen Dimitrios Karkoulis
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    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
10
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg   Pieter Meulenhoff 
11
   Erik Marklund      Teemu Murtola       Szilard Pall       Sander Pronk   
12
   Roland Schulz     Alexey Shvetsov     Michael Shirts     Alfons Sijbers  
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   Peter Tieleman    Teemu Virolainen  Christian Wennberg    Maarten Wolf   
14
                           and the project leaders:
15
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
16

    
17
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
18
Copyright (c) 2001-2017, The GROMACS development team at
19
Uppsala University, Stockholm University and
20
the Royal Institute of Technology, Sweden.
21
check out http://www.gromacs.org for more information.
22

    
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GROMACS is free software; you can redistribute it and/or modify it
24
under the terms of the GNU Lesser General Public License
25
as published by the Free Software Foundation; either version 2.1
26
of the License, or (at your option) any later version.
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GROMACS:      gmx mdrun, version 2018
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Executable:   /opt/tcbsys/gromacs/2018/AVX2_256/bin/gmx
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Data prefix:  /opt/tcbsys/gromacs/2018/AVX2_256
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Working dir:  /nethome/magnusl/tmp/pull_version_test/run
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Command line:
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  gmx mdrun -v -nb gpu -pme gpu -gpu_id 0 -nsteps 50000
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GROMACS version:    2018
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Precision:          single
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Memory model:       64 bit
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MPI library:        thread_mpi
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OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
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GPU support:        CUDA
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SIMD instructions:  AVX2_256
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FFT library:        fftw-3.3.6-pl1-sse2-avx
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RDTSCP usage:       enabled
44
TNG support:        enabled
45
Hwloc support:      hwloc-1.11.0
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Tracing support:    disabled
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Built on:           2018-01-24 18:49:01
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Built by:           viveca@gpu01 [CMAKE]
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Build OS/arch:      Linux 4.4.0-101-generic x86_64
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Build CPU vendor:   Intel
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Build CPU brand:    Intel(R) Xeon(R) CPU           X5650  @ 2.67GHz
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Build CPU family:   6   Model: 44   Stepping: 2
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Build CPU features: aes apic clfsh cmov cx8 cx16 htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3
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C compiler:         /usr/bin/cc GNU 5.4.0
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C compiler flags:    -march=core-avx2     -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
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C++ compiler:       /usr/bin/c++ GNU 5.4.0
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C++ compiler flags:  -march=core-avx2    -std=c++11   -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
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CUDA compiler:      /opt/tcbsys/cuda/8.0/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2016 NVIDIA Corporation;Built on Tue_Jan_10_13:22:03_CST_2017;Cuda compilation tools, release 8.0, V8.0.61
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CUDA compiler flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_60,code=compute_60;-gencode;arch=compute_61,code=compute_61;-use_fast_math;-Wno-deprecated-gpu-targets;-D_FORCE_INLINES;; ;-march=core-avx2;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;
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CUDA driver:        9.0
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CUDA runtime:       8.0
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Running on 1 node with total 24 cores, 48 logical cores, 2 compatible GPUs
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Hardware detected:
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  CPU info:
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    Vendor: Intel
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    Brand:  Intel(R) Xeon(R) CPU E5-2650 v4 @ 2.20GHz
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    Family: 6   Model: 79   Stepping: 1
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    Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
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  Hardware topology: Full, with devices
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    Sockets, cores, and logical processors:
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      Socket  0: [   0  24] [   1  25] [   2  26] [   3  27] [   4  28] [   5  29] [   6  30] [   7  31] [   8  32] [   9  33] [  10  34] [  11  35]
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      Socket  1: [  12  36] [  13  37] [  14  38] [  15  39] [  16  40] [  17  41] [  18  42] [  19  43] [  20  44] [  21  45] [  22  46] [  23  47]
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    Numa nodes:
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      Node  0 (33619877888 bytes mem):   0  24   1  25   2  26   3  27   4  28   5  29   6  30   7  31   8  32   9  33  10  34  11  35
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      Node  1 (33818419200 bytes mem):  12  36  13  37  14  38  15  39  16  40  17  41  18  42  19  43  20  44  21  45  22  46  23  47
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      Latency:
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               0     1
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         0  1.00  2.10
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         1  2.10  1.00
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    Caches:
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      L1: 32768 bytes, linesize 64 bytes, assoc. 8, shared 2 ways
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      L2: 262144 bytes, linesize 64 bytes, assoc. 8, shared 2 ways
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      L3: 31457280 bytes, linesize 64 bytes, assoc. 20, shared 24 ways
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    PCI devices:
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      0000:02:00.0  Id: 10de:1b06  Class: 0x0300  Numa: 0
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      0000:00:11.4  Id: 8086:8d62  Class: 0x0106  Numa: 0
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      0000:03:00.0  Id: 8086:1528  Class: 0x0200  Numa: 0
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      0000:03:00.1  Id: 8086:1528  Class: 0x0200  Numa: 0
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      0000:05:00.0  Id: 1a03:2000  Class: 0x0300  Numa: 0
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      0000:00:1f.2  Id: 8086:8d02  Class: 0x0106  Numa: 0
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      0000:81:00.0  Id: 10de:1b06  Class: 0x0300  Numa: 1
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  GPU info:
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    Number of GPUs detected: 2
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    #0: NVIDIA GeForce GTX 1080 Ti, compute cap.: 6.1, ECC:  no, stat: compatible
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    #1: NVIDIA GeForce GTX 1080 Ti, compute cap.: 6.1, ECC:  no, stat: compatible
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
101
M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
102
Lindahl
103
GROMACS: High performance molecular simulations through multi-level
104
parallelism from laptops to supercomputers
105
SoftwareX 1 (2015) pp. 19-25
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-------- -------- --- Thank You --- -------- --------
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109
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
110
S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
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Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
112
GROMACS
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In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
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Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
120
GROMACS 4.5: a high-throughput and highly parallel open source molecular
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simulation toolkit
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Bioinformatics 29 (2013) pp. 845-54
123
-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
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GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
129
molecular simulation
130
J. Chem. Theory Comput. 4 (2008) pp. 435-447
131
-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
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Berendsen
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GROMACS: Fast, Flexible and Free
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J. Comp. Chem. 26 (2005) pp. 1701-1719
139
-------- -------- --- Thank You --- -------- --------
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141

    
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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E. Lindahl and B. Hess and D. van der Spoel
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GROMACS 3.0: A package for molecular simulation and trajectory analysis
145
J. Mol. Mod. 7 (2001) pp. 306-317
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-------- -------- --- Thank You --- -------- --------
147

    
148

    
149
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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H. J. C. Berendsen, D. van der Spoel and R. van Drunen
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GROMACS: A message-passing parallel molecular dynamics implementation
152
Comp. Phys. Comm. 91 (1995) pp. 43-56
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-------- -------- --- Thank You --- -------- --------
154

    
155
Input Parameters:
156
   integrator                     = md
157
   tinit                          = 0
158
   dt                             = 0.002
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   nsteps                         = 25000000
160
   init-step                      = 0
161
   simulation-part                = 1
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   comm-mode                      = Linear
163
   nstcomm                        = 25
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   bd-fric                        = 0
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   ld-seed                        = -845786280
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   emtol                          = 10
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   emstep                         = 0.01
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   niter                          = 20
169
   fcstep                         = 0
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   nstcgsteep                     = 1000
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   nbfgscorr                      = 10
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   rtpi                           = 0.05
173
   nstxout                        = 0
174
   nstvout                        = 0
175
   nstfout                        = 0
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   nstlog                         = 10000
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   nstcalcenergy                  = 25
178
   nstenergy                      = 25000
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   nstxout-compressed             = 100000
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   compressed-x-precision         = 1000
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   cutoff-scheme                  = Verlet
182
   nstlist                        = 20
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   ns-type                        = Grid
184
   pbc                            = xyz
185
   periodic-molecules             = false
186
   verlet-buffer-tolerance        = 0.005
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   rlist                          = 1.2
188
   coulombtype                    = PME
189
   coulomb-modifier               = Potential-shift
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   rcoulomb-switch                = 0
191
   rcoulomb                       = 1.2
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   epsilon-r                      = 1
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   epsilon-rf                     = inf
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   vdw-type                       = Cut-off
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   vdw-modifier                   = Force-switch
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   rvdw-switch                    = 1
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   rvdw                           = 1.2
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   DispCorr                       = No
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   table-extension                = 1
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   fourierspacing                 = 0.12
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   fourier-nx                     = 40
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   fourier-ny                     = 40
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   fourier-nz                     = 96
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   pme-order                      = 4
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   ewald-rtol                     = 1e-05
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   ewald-rtol-lj                  = 0.001
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   lj-pme-comb-rule               = Geometric
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   ewald-geometry                 = 0
209
   epsilon-surface                = 0
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   implicit-solvent               = No
211
   gb-algorithm                   = Still
212
   nstgbradii                     = 1
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   rgbradii                       = 1
214
   gb-epsilon-solvent             = 80
215
   gb-saltconc                    = 0
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   gb-obc-alpha                   = 1
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   gb-obc-beta                    = 0.8
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   gb-obc-gamma                   = 4.85
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   gb-dielectric-offset           = 0.009
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   sa-algorithm                   = Ace-approximation
221
   sa-surface-tension             = 2.05016
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   tcoupl                         = V-rescale
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   nsttcouple                     = 20
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   nh-chain-length                = 0
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   print-nose-hoover-chain-variables = false
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   pcoupl                         = Parrinello-Rahman
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   pcoupltype                     = Semiisotropic
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   nstpcouple                     = 10
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   tau-p                          = 15
230
   compressibility (3x3):
231
      compressibility[    0]={ 4.50000e-05,  0.00000e+00,  0.00000e+00}
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      compressibility[    1]={ 0.00000e+00,  4.50000e-05,  0.00000e+00}
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      compressibility[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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   ref-p (3x3):
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      ref-p[    0]={ 1.00000e+00,  0.00000e+00,  0.00000e+00}
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      ref-p[    1]={ 0.00000e+00,  1.00000e+00,  0.00000e+00}
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      ref-p[    2]={ 0.00000e+00,  0.00000e+00,  1.00000e+00}
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   refcoord-scaling               = All
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   posres-com (3):
240
      posres-com[0]= 0.00000e+00
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      posres-com[1]= 0.00000e+00
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      posres-com[2]= 0.00000e+00
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   posres-comB (3):
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      posres-comB[0]= 0.00000e+00
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      posres-comB[1]= 0.00000e+00
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      posres-comB[2]= 0.00000e+00
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   QMMM                           = false
248
   QMconstraints                  = 0
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   QMMMscheme                     = 0
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   MMChargeScaleFactor            = 1
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qm-opts:
252
   ngQM                           = 0
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   constraint-algorithm           = Lincs
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   continuation                   = false
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   Shake-SOR                      = false
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   shake-tol                      = 0.0001
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   lincs-order                    = 4
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   lincs-iter                     = 1
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   lincs-warnangle                = 30
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   nwall                          = 0
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   wall-type                      = 9-3
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   wall-r-linpot                  = -1
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   wall-atomtype[0]               = -1
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   wall-atomtype[1]               = -1
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   wall-density[0]                = 0
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   wall-density[1]                = 0
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   wall-ewald-zfac                = 3
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   pull                           = true
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   pull-cylinder-r                = 1.5
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   pull-constr-tol                = 1e-06
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   pull-print-COM                 = false
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   pull-print-ref-value           = false
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   pull-print-components          = false
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   pull-nstxout                   = 10000
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   pull-nstfout                   = 100
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   pull-ngroups                   = 4
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   pull-group 0:
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     atom: not available
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     weight: not available
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     pbcatom                        = -1
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   pull-group 1:
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     atom (26482):
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        atom[0,...,26481] = {0,...,26481}
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     weight: not available
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     pbcatom                        = 24390
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   pull-group 2:
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     atom (49):
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        atom[0,...,48] = {26482,...,26530}
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     weight: not available
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     pbcatom                        = 26506
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   pull-group 3:
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     atom (49):
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        atom[0,...,48] = {26531,...,26579}
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     weight: not available
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     pbcatom                        = 26555
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   pull-ncoords                   = 2
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   pull-coord 0:
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   type                           = constraint
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   geometry                       = direction-periodic
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   group[0]                       = 1
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   group[1]                       = 2
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   dim (3):
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      dim[0]=0
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      dim[1]=0
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      dim[2]=1
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   origin (3):
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      origin[0]= 0.00000e+00
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      origin[1]= 0.00000e+00
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      origin[2]= 0.00000e+00
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   vec (3):
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      vec[0]= 0.00000e+00
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      vec[1]= 0.00000e+00
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      vec[2]= 1.00000e+00
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   start                          = true
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   init                           = 5.19776
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   rate                           = 0.000209
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   k                              = 0
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   kB                             = 0
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   pull-coord 1:
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   type                           = constraint
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   geometry                       = direction-periodic
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   group[0]                       = 1
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   group[1]                       = 3
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   dim (3):
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      dim[0]=0
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      dim[1]=0
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      dim[2]=1
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   origin (3):
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      origin[0]= 0.00000e+00
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      origin[1]= 0.00000e+00
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      origin[2]= 0.00000e+00
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   vec (3):
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      vec[0]= 0.00000e+00
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      vec[1]= 0.00000e+00
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      vec[2]= 1.00000e+00
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   start                          = true
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   init                           = 0.0448105
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   rate                           = 0.000209
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   k                              = 0
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   kB                             = 0
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   awh                            = false
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   rotation                       = false
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   interactiveMD                  = false
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   disre                          = No
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   disre-weighting                = Conservative
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   disre-mixed                    = false
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   dr-fc                          = 1000
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   dr-tau                         = 0
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   nstdisreout                    = 100
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   orire-fc                       = 0
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   orire-tau                      = 0
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   nstorireout                    = 100
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   free-energy                    = no
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   cos-acceleration               = 0
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   deform (3x3):
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      deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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   simulated-tempering            = false
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   swapcoords                     = no
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   userint1                       = 0
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   userint2                       = 0
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   userint3                       = 0
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   userint4                       = 0
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   userreal1                      = 0
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   userreal2                      = 0
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   userreal3                      = 0
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   userreal4                      = 0
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   applied-forces:
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     electric-field:
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       x:
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         E0                       = 0
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         omega                    = 0
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         t0                       = 0
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         sigma                    = 0
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       y:
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         E0                       = 0
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         omega                    = 0
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         t0                       = 0
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         sigma                    = 0
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       z:
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         E0                       = 0
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         omega                    = 0
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         t0                       = 0
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         sigma                    = 0
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grpopts:
387
   nrdf:       62655
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   ref-t:      303.15
389
   tau-t:         0.2
390
annealing:          No
391
annealing-npoints:           0
392
   acc:	           0           0           0
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   nfreeze:           N           N           N
394
   energygrp-flags[  0]: 0
395

    
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The -nsteps functionality is deprecated, and may be removed in a future version. Consider using gmx convert-tpr -nsteps or changing the appropriate .mdp file field.
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Overriding nsteps with value passed on the command line: 50000 steps, 100 ps
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Changing nstlist from 20 to 100, rlist from 1.2 to 1.281
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Using 1 MPI thread
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Using 24 OpenMP threads 
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1 GPU auto-selected for this run.
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Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:
407
  PP:0,PME:0
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Pinning threads with an auto-selected logical core stride of 2
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System total charge: 0.000
410
Will do PME sum in reciprocal space for electrostatic interactions.
411

    
412
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
413
U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
414
A smooth particle mesh Ewald method
415
J. Chem. Phys. 103 (1995) pp. 8577-8592
416
-------- -------- --- Thank You --- -------- --------
417

    
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Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
419
Potential shift: LJ r^-12: -2.648e-01 r^-6: -5.349e-01, Ewald -8.333e-06
420
Initialized non-bonded Ewald correction tables, spacing: 1.02e-03 size: 1176
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422
Generated table with 1140 data points for 1-4 COUL.
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Tabscale = 500 points/nm
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Generated table with 1140 data points for 1-4 LJ6.
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Tabscale = 500 points/nm
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Generated table with 1140 data points for 1-4 LJ12.
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Tabscale = 500 points/nm
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429
Using GPU 8x8 nonbonded short-range kernels
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431
Using a dual 8x4 pair-list setup updated with dynamic, rolling pruning:
432
  outer list: updated every 100 steps, buffer 0.081 nm, rlist 1.281 nm
433
  inner list: updated every  52 steps, buffer 0.004 nm, rlist 1.204 nm
434
At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
435
  outer list: updated every 100 steps, buffer 0.241 nm, rlist 1.441 nm
436
  inner list: updated every  52 steps, buffer 0.144 nm, rlist 1.344 nm
437

    
438
Removing pbc first time
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440
Will apply constraint COM pulling
441
with 2 pull coordinates and 3 groups
442
Pull group 1: 26482 atoms, mass 134761.866
443
Pull group 2:    49 atoms, mass   288.431
444
Pull group 3:    49 atoms, mass   288.431
445

    
446
Initializing LINear Constraint Solver
447

    
448
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
449
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
450
LINCS: A Linear Constraint Solver for molecular simulations
451
J. Comp. Chem. 18 (1997) pp. 1463-1472
452
-------- -------- --- Thank You --- -------- --------
453

    
454
The number of constraints is 16810
455

    
456
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
457
S. Miyamoto and P. A. Kollman
458
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
459
Water Models
460
J. Comp. Chem. 13 (1992) pp. 952-962
461
-------- -------- --- Thank You --- -------- --------
462

    
463

    
464
Intra-simulation communication will occur every 5 steps.
465
Center of mass motion removal mode is Linear
466
We have the following groups for center of mass motion removal:
467
  0:  System
468

    
469
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
470
G. Bussi, D. Donadio and M. Parrinello
471
Canonical sampling through velocity rescaling
472
J. Chem. Phys. 126 (2007) pp. 014101
473
-------- -------- --- Thank You --- -------- --------
474

    
475
There are: 26580 Atoms
476

    
477
Constraining the starting coordinates (step 0)
478

    
479
Constraining the coordinates at t0-dt (step 0)
480
RMS relative constraint deviation after constraining: 3.12e-06
481
Initial temperature: 301.982 K
482

    
483
Started mdrun on rank 0 Fri Feb  2 10:56:36 2018
484
           Step           Time
485
              0        0.00000
486

    
487
   Energies (kJ/mol)
488
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
489
    1.24914e+04    6.30414e+04    3.97602e+04    2.66369e+02    5.34080e+03
490
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
491
   -9.83236e+03   -4.85576e+04   -4.30629e+04    8.63634e+02    2.03109e+04
492
    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
493
    7.88495e+04    9.91604e+04    9.91743e+04    3.02719e+02    1.92924e+02
494
   Constr. rmsd
495
    3.13929e-06
496

    
497
step  200: timed with pme grid 40 40 96, coulomb cutoff 1.200: 284.8 M-cycles
498
step  400: timed with pme grid 40 36 84, coulomb cutoff 1.280: 271.8 M-cycles
499
step  600: timed with pme grid 36 32 72, coulomb cutoff 1.449: 298.9 M-cycles
500
step  800: timed with pme grid 32 28 64, coulomb cutoff 1.645: 337.8 M-cycles
501
step 1000: timed with pme grid 32 32 64, coulomb cutoff 1.630: 354.3 M-cycles
502
step 1200: timed with pme grid 32 32 72, coulomb cutoff 1.500: 299.6 M-cycles
503
step 1400: timed with pme grid 36 32 72, coulomb cutoff 1.449: 286.8 M-cycles
504
step 1600: timed with pme grid 36 32 80, coulomb cutoff 1.440: 284.3 M-cycles
505
step 1800: timed with pme grid 36 36 80, coulomb cutoff 1.333: 263.0 M-cycles
506
step 2000: timed with pme grid 40 36 80, coulomb cutoff 1.304: 259.3 M-cycles
507
step 2200: timed with pme grid 40 36 84, coulomb cutoff 1.280: 256.9 M-cycles
508
step 2400: timed with pme grid 40 40 84, coulomb cutoff 1.242: 252.2 M-cycles
509
step 2600: timed with pme grid 40 40 96, coulomb cutoff 1.200: 240.8 M-cycles
510
step 2800: timed with pme grid 36 36 80, coulomb cutoff 1.333: 273.8 M-cycles
511
step 3000: timed with pme grid 40 36 80, coulomb cutoff 1.304: 281.6 M-cycles
512
step 3200: timed with pme grid 40 36 84, coulomb cutoff 1.280: 276.1 M-cycles
513
step 3400: timed with pme grid 40 40 84, coulomb cutoff 1.242: 270.6 M-cycles
514
step 3600: timed with pme grid 40 40 96, coulomb cutoff 1.200: 259.5 M-cycles
515
              optimal pme grid 40 40 96, coulomb cutoff 1.200
516
           Step           Time
517
          10000       20.00000
518

    
519
   Energies (kJ/mol)
520
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
521
    1.19086e+04    6.25871e+04    3.98040e+04    2.28925e+02    5.46809e+03
522
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
523
   -1.00557e+04   -4.83749e+04   -4.30648e+04    8.38834e+02    1.93400e+04
524
    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
525
    7.93588e+04    9.86988e+04    1.02457e+05    3.04674e+02    3.26484e+01
526
   Constr. rmsd
527
    3.12392e-06
528

    
529
           Step           Time
530
          20000       40.00000
531

    
532
   Energies (kJ/mol)
533
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
534
    1.20230e+04    6.19609e+04    4.00111e+04    2.42756e+02    5.43758e+03
535
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
536
   -1.04084e+04   -4.86871e+04   -4.25633e+04    8.74951e+02    1.88915e+04
537
    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
538
    7.87912e+04    9.76827e+04    1.05078e+05    3.02495e+02   -8.04947e+01
539
   Constr. rmsd
540
    3.06934e-06
541

    
542
           Step           Time
543
          30000       60.00000
544

    
545
   Energies (kJ/mol)
546
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
547
    1.21840e+04    6.28769e+04    4.00853e+04    2.40411e+02    5.41733e+03
548
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
549
   -9.98016e+03   -4.83150e+04   -4.29539e+04    8.26015e+02    2.03809e+04
550
    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
551
    7.96675e+04    1.00048e+05    1.08488e+05    3.05859e+02   -2.42951e+02
552
   Constr. rmsd
553
    3.09065e-06
554

    
555
           Step           Time
556
          40000       80.00000
557

    
558
   Energies (kJ/mol)
559
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
560
    1.22239e+04    6.24328e+04    3.97028e+04    2.51712e+02    5.38617e+03
561
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
562
   -9.99882e+03   -4.81352e+04   -4.28559e+04    8.35736e+02    1.98431e+04
563
    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
564
    7.84681e+04    9.83112e+04    1.10997e+05    3.01254e+02   -1.47226e+01
565
   Constr. rmsd
566
    3.13442e-06
567

    
568
           Step           Time
569
          50000      100.00000
570

    
571
Writing checkpoint, step 50000 at Fri Feb  2 10:57:43 2018
572

    
573

    
574

    
575

    
576
-----------------------------------------------------------
577
Restarting from checkpoint, appending to previous log file.
578

    
579
Log file opened on Fri Feb  2 14:10:15 2018
580
Host: nid01639  pid: 31832  rank ID: 0  number of ranks:  32
581
                       :-) GROMACS - gmx mdrun, 2018 (-:
582

    
583
Executable:   /pdc/vol/gromacs/2018.1/bin/gmx_mpi
584
Data prefix:  /pdc/vol/gromacs/2018.1
585
Working dir:  /cfs/klemming/nobackup/m/malu6955/tmp/pull_version_test/run
586
Command line:
587
  gmx_mpi mdrun -cpi -nsteps 100000
588

    
589
GROMACS version:    2018
590
Precision:          single
591
Memory model:       64 bit
592
MPI library:        MPI
593
OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
594
GPU support:        disabled
595
SIMD instructions:  AVX2_256
596
FFT library:        commercial-fftw-3.3.4-fma-sse2-avx-avx2
597
RDTSCP usage:       enabled
598
TNG support:        enabled
599
Hwloc support:      disabled
600
Tracing support:    disabled
601
Built on:           2018-02-02 12:31:21
602
Built by:           kthw@beskow-login2.pdc.kth.se [CMAKE]
603
Build OS/arch:      Linux 3.0.101-0.46.1_1.0502.8871-cray_ari_s x86_64
604
Build CPU vendor:   Unknown
605
Build CPU brand:    Unknown
606
Build CPU family:   0   Model: 0   Stepping: 0
607
Build CPU features: Unknown
608
C compiler:         /opt/cray/craype/2.5.13/bin/cc GNU 7.2.0
609
C compiler flags:    -march=core-avx2     -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
610
C++ compiler:       /opt/cray/craype/2.5.13/bin/CC GNU 7.2.0
611
C++ compiler flags:  -march=core-avx2    -std=c++11   -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
612

    
613
The -nsteps functionality is deprecated, and may be removed in a future version. Consider using gmx convert-tpr -nsteps or changing the appropriate .mdp file field.
614

    
615
Overriding nsteps with value passed on the command line: 100000 steps, 200 ps
616
Changing nstlist from 20 to 100, rlist from 1.2 to 1.281
617

    
618

    
619
Initializing Domain Decomposition on 32 ranks
620
Dynamic load balancing: locked
621
Initial maximum inter charge-group distances:
622
    two-body bonded interactions: 0.492 nm, Exclusion, atoms 8889 8893
623
  multi-body bonded interactions: 0.416 nm, Proper Dih., atoms 5274 5284
624
Minimum cell size due to bonded interactions: 0.458 nm
625
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.222 nm
626
Estimated maximum distance required for P-LINCS: 0.222 nm
627
Guess for relative PME load: 0.11
628
Will use 24 particle-particle and 8 PME only ranks
629
This is a guess, check the performance at the end of the log file
630
Using 8 separate PME ranks, as guessed by mdrun
631
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
632
Optimizing the DD grid for 24 cells with a minimum initial size of 0.572 nm
633
The maximum allowed number of cells is: X 8 Y 8 Z 18
634
Domain decomposition grid 4 x 2 x 3, separate PME ranks 8
635
PME domain decomposition: 4 x 2 x 1
636
Interleaving PP and PME ranks
637
This rank does only particle-particle work.
638

    
639
Domain decomposition rank 0, coordinates 0 0 0
640

    
641
The initial number of communication pulses is: X 2 Y 1 Z 1
642
The initial domain decomposition cell size is: X 1.20 nm Y 2.31 nm Z 3.48 nm
643

    
644
The maximum allowed distance for charge groups involved in interactions is:
645
                 non-bonded interactions           1.281 nm
646
(the following are initial values, they could change due to box deformation)
647
            two-body bonded interactions  (-rdd)   1.281 nm
648
          multi-body bonded interactions  (-rdd)   1.202 nm
649
  atoms separated by up to 5 constraints  (-rcon)  1.202 nm
650

    
651
When dynamic load balancing gets turned on, these settings will change to:
652
The maximum number of communication pulses is: X 2 Y 1 Z 2
653
The minimum size for domain decomposition cells is 0.809 nm
654
The requested allowed shrink of DD cells (option -dds) is: 0.80
655
The allowed shrink of domain decomposition cells is: X 0.67 Y 0.56 Z 0.23
656
The maximum allowed distance for charge groups involved in interactions is:
657
                 non-bonded interactions           1.281 nm
658
            two-body bonded interactions  (-rdd)   1.281 nm
659
          multi-body bonded interactions  (-rdd)   0.809 nm
660
  atoms separated by up to 5 constraints  (-rcon)  0.809 nm
661

    
662
Using two step summing over 2 groups of on average 12.0 ranks
663

    
664

    
665
Using 32 MPI processes
666
Using 2 OpenMP threads per MPI process
667

    
668

    
669
NOTE: The number of threads is not equal to the number of (logical) cores
670
      and the -pin option is set to auto: will not pin threads to cores.
671
      This can lead to significant performance degradation.
672
      Consider using -pin on (and -pinoffset in case you run multiple jobs).
673
System total charge: 0.000
674
Will do PME sum in reciprocal space for electrostatic interactions.
675

    
676
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
677
U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
678
A smooth particle mesh Ewald method
679
J. Chem. Phys. 103 (1995) pp. 8577-8592
680
-------- -------- --- Thank You --- -------- --------
681

    
682
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
683
Potential shift: LJ r^-12: -2.648e-01 r^-6: -5.349e-01, Ewald -8.333e-06
684
Initialized non-bonded Ewald correction tables, spacing: 1.02e-03 size: 1176
685

    
686
Generated table with 1140 data points for 1-4 COUL.
687
Tabscale = 500 points/nm
688
Generated table with 1140 data points for 1-4 LJ6.
689
Tabscale = 500 points/nm
690
Generated table with 1140 data points for 1-4 LJ12.
691
Tabscale = 500 points/nm
692

    
693
Using SIMD 4x8 nonbonded short-range kernels
694

    
695
Using a dual 4x8 pair-list setup updated with dynamic pruning:
696
  outer list: updated every 100 steps, buffer 0.081 nm, rlist 1.281 nm
697
  inner list: updated every  53 steps, buffer 0.002 nm, rlist 1.202 nm
698
At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
699
  outer list: updated every 100 steps, buffer 0.241 nm, rlist 1.441 nm
700
  inner list: updated every  53 steps, buffer 0.143 nm, rlist 1.343 nm
701

    
702

    
703
Will apply constraint COM pulling
704
with 2 pull coordinates and 3 groups
705
Pull group 1: 26482 atoms, mass 134761.866
706
Pull group 2:    49 atoms, mass   288.431
707
Pull group 3:    49 atoms, mass   288.431
708

    
709
Initializing Parallel LINear Constraint Solver
710

    
711
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
712
B. Hess
713
P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
714
J. Chem. Theory Comput. 4 (2008) pp. 116-122
715
-------- -------- --- Thank You --- -------- --------
716

    
717
The number of constraints is 16810
718
There are inter charge-group constraints,
719
will communicate selected coordinates each lincs iteration
720

    
721
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
722
S. Miyamoto and P. A. Kollman
723
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
724
Water Models
725
J. Comp. Chem. 13 (1992) pp. 952-962
726
-------- -------- --- Thank You --- -------- --------
727

    
728

    
729
Linking all bonded interactions to atoms
730

    
731

    
732
Intra-simulation communication will occur every 5 steps.
733
Center of mass motion removal mode is Linear
734
We have the following groups for center of mass motion removal:
735
  0:  System
736
There are: 26580 Atoms
737
Atom distribution over 24 domains: av 1107 stddev 38 min 1047 max 1140
738

    
739
Started mdrun on rank 0 Fri Feb  2 14:10:15 2018
740
           Step           Time
741
          50000      100.00000
742

    
743
   Energies (kJ/mol)
744
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
745
    1.19529e+04    6.16190e+04    4.01029e+04    2.31259e+02    5.36104e+03
746
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
747
   -9.55675e+03   -4.83057e+04   -4.34152e+04    8.64949e+02    1.88544e+04
748
    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
749
    7.85457e+04    9.74001e+04    1.13739e+05    3.01552e+02   -3.31722e+02
750
   Constr. rmsd
751
    3.06520e-06
752

    
753
DD  step 50099 load imb.: force 32.6%  pme mesh/force 0.653
754

    
755

    
756
step 50300 Turning on dynamic load balancing, because the performance loss due to load imbalance is 4.7 %.
757

    
758

    
759
step 54000 Turning off dynamic load balancing, because it is degrading performance.
760

    
761
Atom distribution over 24 domains: av 1107 stddev 42 min 1018 max 1153
762
DD  step 59999 load imb.: force  5.3%  pme mesh/force 0.953
763

    
764

    
765
step 60000 Turning on dynamic load balancing, because the performance loss due to load imbalance is 2.4 %.
766

    
767
           Step           Time
768
          60000      120.00000
769

    
770
   Energies (kJ/mol)
771
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
772
    1.18368e+04    6.25889e+04    4.00397e+04    2.51424e+02    5.48902e+03
773
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
774
   -1.02450e+04   -4.84572e+04   -4.29541e+04    8.65839e+02    1.94154e+04
775
    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
776
    7.91998e+04    9.86152e+04    2.15608e+05    3.04063e+02    4.08647e+02
777
   Constr. rmsd
778
    3.07939e-06
779

    
780
DD  step 69999  vol min/aver 0.932  load imb.: force  1.8%  pme mesh/force 0.865
781

    
782
           Step           Time
783
          70000      140.00000
784

    
785
   Energies (kJ/mol)
786
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
787
    1.23205e+04    6.18288e+04    3.97656e+04    2.53127e+02    5.28473e+03
788
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
789
   -1.02574e+04   -4.83433e+04   -4.26236e+04    8.52439e+02    1.90809e+04
790
    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
791
    1.23402e+05    1.42483e+05    4.26230e+05    4.73765e+02    1.56703e+03
792
   Constr. rmsd
793
    3.11190e-06
794

    
795
DD  step 79999  vol min/aver 0.919  load imb.: force  1.8%  pme mesh/force 0.477
796

    
797
           Step           Time
798
          80000      160.00000
799

    
800
   Energies (kJ/mol)
801
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
802
    1.21553e+04    6.29020e+04    4.01354e+04    2.15303e+02    5.40688e+03
803
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
804
   -1.03327e+04   -4.84215e+04   -4.24987e+04    8.74507e+02    2.04365e+04
805
    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
806
    7.90885e+04    9.95250e+04    4.98788e+05    3.03636e+02   -3.84807e+02
807
   Constr. rmsd
808
    3.14393e-06
809

    
810
DD  step 89999  vol min/aver 0.918  load imb.: force  2.2%  pme mesh/force 0.806
811

    
812
           Step           Time
813
          90000      180.00000
814

    
815
   Energies (kJ/mol)
816
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
817
    1.20786e+04    6.17484e+04    3.98113e+04    2.39955e+02    5.36043e+03
818
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
819
   -1.04712e+04   -4.85203e+04   -4.32276e+04    8.29305e+02    1.78489e+04
820
    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
821
    8.36001e+04    1.01449e+05    5.69796e+05    3.20957e+02    3.58311e+02
822
   Constr. rmsd
823
    3.01773e-06
824

    
825
DD  step 99999  vol min/aver 0.936  load imb.: force  2.1%  pme mesh/force 0.686
826

    
827
           Step           Time
828
         100000      200.00000
829

    
830
   Energies (kJ/mol)
831
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
832
    1.18732e+04    6.13914e+04    3.96481e+04    2.09627e+02    5.46381e+03
833
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
834
   -1.03423e+04   -4.86539e+04   -4.29085e+04    8.36474e+02    1.75181e+04
835
    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
836
    7.88806e+04    9.63988e+04    6.16765e+05    3.02838e+02    2.59214e+02
837
   Constr. rmsd
838
    3.02292e-06
839

    
840
DD  step 109999  vol min/aver 0.936  load imb.: force  2.2%  pme mesh/force 0.836
841

    
842
           Step           Time
843
         110000      220.00000
844

    
845
   Energies (kJ/mol)
846
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
847
    1.20092e+04    6.12697e+04    3.98919e+04    2.42246e+02    5.41819e+03
848
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
849
   -1.04857e+04   -4.88591e+04   -4.25572e+04    8.50660e+02    1.77798e+04
850
    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
851
    7.77151e+04    9.54949e+04    7.82588e+05    2.98363e+02    4.14033e+02
852
   Constr. rmsd
853
    3.12187e-06
854

    
855
DD  step 119999  vol min/aver 0.925  load imb.: force  2.5%  pme mesh/force 0.477
856

    
857
           Step           Time
858
         120000      240.00000
859

    
860
   Energies (kJ/mol)
861
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
862
    1.19701e+04    6.18903e+04    4.00055e+04    2.77714e+02    5.47177e+03
863
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
864
   -1.00957e+04   -4.85272e+04   -4.28652e+04    8.50012e+02    1.89773e+04
865
    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
866
    1.03867e+05    1.22845e+05    1.02911e+06    3.98767e+02    1.24582e+03
867
   Constr. rmsd
868
    3.07211e-06
869

    
870
DD  step 129999  vol min/aver 0.915  load imb.: force  1.9%  pme mesh/force 0.434
871

    
872
           Step           Time
873
         130000      260.00000
874

    
875
   Energies (kJ/mol)
876
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
877
    1.21021e+04    6.21912e+04    3.98851e+04    2.36477e+02    5.40276e+03
878
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
879
   -1.02507e+04   -4.84209e+04   -4.29969e+04    8.67113e+02    1.90161e+04
880
    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
881
    7.85418e+04    9.75579e+04    1.18702e+06    3.01537e+02   -5.44848e+01
882
   Constr. rmsd
883
    3.10114e-06
884

    
885
DD  step 139999  vol min/aver 0.914  load imb.: force  1.7%  pme mesh/force 0.474
886

    
887
           Step           Time
888
         140000      280.00000
889

    
890
   Energies (kJ/mol)
891
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
892
    1.16451e+04    6.04166e+04    3.97936e+04    2.47529e+02    5.41062e+03
893
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
894
   -1.06786e+04   -4.85398e+04   -4.29141e+04    8.19714e+02    1.62006e+04
895
    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
896
    1.14069e+05    1.30269e+05    1.38599e+06    4.37931e+02    1.77936e+03
897
   Constr. rmsd
898
    2.91106e-06
899

    
900
DD  step 149999  vol min/aver 0.932  load imb.: force  2.2%  pme mesh/force 0.629
901

    
902
           Step           Time
903
         150000      300.00000
904

    
905
Writing checkpoint, step 150000 at Fri Feb  2 14:14:58 2018
906

    
907

    
908

    
909

    
910
-----------------------------------------------------------
911
Restarting from checkpoint, appending to previous log file.
912

    
913
Log file opened on Fri Feb  2 14:17:57 2018
914
Host: erco-gpu17  pid: 9952  rank ID: 0  number of ranks:  1
915
                       :-) GROMACS - gmx mdrun, 2018 (-:
916

    
917
Executable:   /opt/tcbsys/gromacs/2018/AVX2_256/bin/gmx
918
Data prefix:  /opt/tcbsys/gromacs/2018/AVX2_256
919
Working dir:  /nethome/magnusl/tmp/pull_version_test/run
920
Command line:
921
  gmx mdrun -v -nb gpu -pme gpu -gpu_id 0 -nsteps 100000 -cpi
922

    
923
GROMACS version:    2018
924
Precision:          single
925
Memory model:       64 bit
926
MPI library:        thread_mpi
927
OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
928
GPU support:        CUDA
929
SIMD instructions:  AVX2_256
930
FFT library:        fftw-3.3.6-pl1-sse2-avx
931
RDTSCP usage:       enabled
932
TNG support:        enabled
933
Hwloc support:      hwloc-1.11.0
934
Tracing support:    disabled
935
Built on:           2018-01-24 18:49:01
936
Built by:           viveca@gpu01 [CMAKE]
937
Build OS/arch:      Linux 4.4.0-101-generic x86_64
938
Build CPU vendor:   Intel
939
Build CPU brand:    Intel(R) Xeon(R) CPU           X5650  @ 2.67GHz
940
Build CPU family:   6   Model: 44   Stepping: 2
941
Build CPU features: aes apic clfsh cmov cx8 cx16 htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3
942
C compiler:         /usr/bin/cc GNU 5.4.0
943
C compiler flags:    -march=core-avx2     -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
944
C++ compiler:       /usr/bin/c++ GNU 5.4.0
945
C++ compiler flags:  -march=core-avx2    -std=c++11   -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
946
CUDA compiler:      /opt/tcbsys/cuda/8.0/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2016 NVIDIA Corporation;Built on Tue_Jan_10_13:22:03_CST_2017;Cuda compilation tools, release 8.0, V8.0.61
947
CUDA compiler flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_60,code=compute_60;-gencode;arch=compute_61,code=compute_61;-use_fast_math;-Wno-deprecated-gpu-targets;-D_FORCE_INLINES;; ;-march=core-avx2;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;
948
CUDA driver:        9.0
949
CUDA runtime:       8.0
950

    
951
The -nsteps functionality is deprecated, and may be removed in a future version. Consider using gmx convert-tpr -nsteps or changing the appropriate .mdp file field.
952

    
953
Overriding nsteps with value passed on the command line: 100000 steps, 200 ps
954
Changing nstlist from 20 to 100, rlist from 1.2 to 1.281
955

    
956

    
957
Using 1 MPI thread
958
Using 24 OpenMP threads 
959

    
960
1 GPU auto-selected for this run.
961
Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:
962
  PP:0,PME:0
963
Pinning threads with an auto-selected logical core stride of 2
964
System total charge: 0.000
965
Will do PME sum in reciprocal space for electrostatic interactions.
966

    
967
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
968
U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
969
A smooth particle mesh Ewald method
970
J. Chem. Phys. 103 (1995) pp. 8577-8592
971
-------- -------- --- Thank You --- -------- --------
972

    
973
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
974
Potential shift: LJ r^-12: -2.648e-01 r^-6: -5.349e-01, Ewald -8.333e-06
975
Initialized non-bonded Ewald correction tables, spacing: 1.02e-03 size: 1176
976

    
977
Generated table with 1140 data points for 1-4 COUL.
978
Tabscale = 500 points/nm
979
Generated table with 1140 data points for 1-4 LJ6.
980
Tabscale = 500 points/nm
981
Generated table with 1140 data points for 1-4 LJ12.
982
Tabscale = 500 points/nm
983

    
984
Using GPU 8x8 nonbonded short-range kernels
985

    
986
Using a dual 8x4 pair-list setup updated with dynamic, rolling pruning:
987
  outer list: updated every 100 steps, buffer 0.081 nm, rlist 1.281 nm
988
  inner list: updated every  52 steps, buffer 0.004 nm, rlist 1.204 nm
989
At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
990
  outer list: updated every 100 steps, buffer 0.241 nm, rlist 1.441 nm
991
  inner list: updated every  52 steps, buffer 0.143 nm, rlist 1.343 nm
992

    
993

    
994
Will apply constraint COM pulling
995
with 2 pull coordinates and 3 groups
996
Pull group 1: 26482 atoms, mass 134761.866
997
Pull group 2:    49 atoms, mass   288.431
998
Pull group 3:    49 atoms, mass   288.431
999

    
1000
Initializing LINear Constraint Solver
1001

    
1002
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
1003
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
1004
LINCS: A Linear Constraint Solver for molecular simulations
1005
J. Comp. Chem. 18 (1997) pp. 1463-1472
1006
-------- -------- --- Thank You --- -------- --------
1007

    
1008
The number of constraints is 16810
1009

    
1010
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
1011
S. Miyamoto and P. A. Kollman
1012
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
1013
Water Models
1014
J. Comp. Chem. 13 (1992) pp. 952-962
1015
-------- -------- --- Thank You --- -------- --------
1016

    
1017

    
1018
Intra-simulation communication will occur every 5 steps.
1019
Center of mass motion removal mode is Linear
1020
We have the following groups for center of mass motion removal:
1021
  0:  System
1022
There are: 26580 Atoms
1023

    
1024
Started mdrun on rank 0 Fri Feb  2 14:18:00 2018
1025
           Step           Time
1026
         150000      300.00000
1027

    
1028
   Energies (kJ/mol)
1029
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
1030
    1.18443e+04    6.09737e+04    3.94505e+04    2.14953e+02    5.45974e+03
1031
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
1032
   -1.04050e+04   -4.82432e+04   -4.26023e+04    8.59488e+02    1.75521e+04
1033
    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
1034
    7.80254e+04    9.55775e+04    1.45504e+06    2.99555e+02    1.51446e+02
1035
   Constr. rmsd
1036
    3.01571e-06
1037

    
1038
step 150200: timed with pme grid 40 40 96, coulomb cutoff 1.200: 281.6 M-cycles
1039
step 150400: timed with pme grid 40 36 84, coulomb cutoff 1.282: 287.9 M-cycles
1040
step 150600: timed with pme grid 36 32 72, coulomb cutoff 1.449: 288.3 M-cycles
1041
step 150800: timed with pme grid 32 28 64, coulomb cutoff 1.648: 339.4 M-cycles
1042
step 151000: timed with pme grid 32 32 64, coulomb cutoff 1.630: 334.1 M-cycles
1043
step 151200: timed with pme grid 32 32 72, coulomb cutoff 1.503: 298.4 M-cycles
1044
step 151400: timed with pme grid 36 32 72, coulomb cutoff 1.449: 286.6 M-cycles
1045
step 151600: timed with pme grid 36 32 80, coulomb cutoff 1.442: 286.1 M-cycles
1046
step 151800: timed with pme grid 36 36 80, coulomb cutoff 1.336: 263.2 M-cycles
1047
step 152000: timed with pme grid 40 36 80, coulomb cutoff 1.304: 261.0 M-cycles
1048
step 152200: timed with pme grid 40 36 84, coulomb cutoff 1.282: 271.0 M-cycles
1049
step 152400: timed with pme grid 40 40 84, coulomb cutoff 1.242: 250.1 M-cycles
1050
step 152600: timed with pme grid 40 40 96, coulomb cutoff 1.200: 261.3 M-cycles
1051
step 152800: timed with pme grid 36 36 80, coulomb cutoff 1.336: 287.1 M-cycles
1052
step 153000: timed with pme grid 40 36 80, coulomb cutoff 1.304: 262.7 M-cycles
1053
step 153200: timed with pme grid 40 36 84, coulomb cutoff 1.282: 258.6 M-cycles
1054
step 153400: timed with pme grid 40 40 84, coulomb cutoff 1.242: 250.9 M-cycles
1055
step 153600: timed with pme grid 40 40 96, coulomb cutoff 1.200: 241.6 M-cycles
1056
step 153800: timed with pme grid 36 36 80, coulomb cutoff 1.336: 289.0 M-cycles
1057
step 154000: timed with pme grid 40 36 80, coulomb cutoff 1.304: 263.1 M-cycles
1058
step 154200: timed with pme grid 40 36 84, coulomb cutoff 1.282: 258.0 M-cycles
1059
step 154400: timed with pme grid 40 40 84, coulomb cutoff 1.242: 255.9 M-cycles
1060
step 154600: timed with pme grid 40 40 96, coulomb cutoff 1.200: 256.2 M-cycles
1061
              optimal pme grid 40 40 96, coulomb cutoff 1.200
1062
           Step           Time
1063
         160000      320.00000
1064

    
1065
   Energies (kJ/mol)
1066
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
1067
    1.23102e+04    6.22208e+04    3.97754e+04    2.29636e+02    5.29775e+03
1068
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
1069
   -1.02741e+04   -4.86647e+04   -4.24225e+04    8.27675e+02    1.93000e+04
1070
    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
1071
    7.85623e+04    9.78623e+04    1.45733e+06    3.01616e+02   -1.67181e+02
1072
   Constr. rmsd
1073
    3.10686e-06
1074

    
1075
           Step           Time
1076
         170000      340.00000
1077

    
1078
   Energies (kJ/mol)
1079
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
1080
    1.20158e+04    6.26042e+04    4.02043e+04    2.32636e+02    5.43110e+03
1081
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
1082
   -1.05497e+04   -4.85357e+04   -4.27194e+04    8.70415e+02    1.95536e+04
1083
    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
1084
    7.88119e+04    9.83655e+04    1.45956e+06    3.02574e+02    5.79801e+02
1085
   Constr. rmsd
1086
    3.06852e-06
1087

    
1088
           Step           Time
1089
         180000      360.00000
1090

    
1091
   Energies (kJ/mol)
1092
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
1093
    1.21465e+04    6.21659e+04    3.98974e+04    2.79447e+02    5.44310e+03
1094
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
1095
   -1.02223e+04   -4.81291e+04   -4.30914e+04    8.45991e+02    1.93355e+04
1096
    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
1097
    7.88856e+04    9.82211e+04    1.46321e+06    3.02857e+02    1.93926e+02
1098
   Constr. rmsd
1099
    3.09303e-06
1100

    
1101
           Step           Time
1102
         190000      380.00000
1103

    
1104
   Energies (kJ/mol)
1105
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
1106
    1.19421e+04    6.25402e+04    4.01221e+04    2.45313e+02    5.51645e+03
1107
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
1108
   -1.03047e+04   -4.85722e+04   -4.23602e+04    8.67818e+02    1.99969e+04
1109
    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
1110
    7.88505e+04    9.88474e+04    1.46601e+06    3.02722e+02    1.46879e+02
1111
   Constr. rmsd
1112
    3.11600e-06
1113

    
1114
           Step           Time
1115
         200000      400.00000
1116

    
1117
   Energies (kJ/mol)
1118
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
1119
    1.17102e+04    6.20476e+04    3.98128e+04    2.48440e+02    5.37409e+03
1120
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
1121
   -1.02067e+04   -4.83263e+04   -4.27611e+04    8.71570e+02    1.87707e+04
1122
    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
1123
    7.90918e+04    9.78625e+04    1.46909e+06    3.03649e+02    3.50597e+02
1124
   Constr. rmsd
1125
    3.17711e-06
1126

    
1127
           Step           Time
1128
         210000      420.00000
1129

    
1130
   Energies (kJ/mol)
1131
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
1132
    1.20836e+04    6.21483e+04    4.00392e+04    2.55119e+02    5.26674e+03
1133
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
1134
   -9.94401e+03   -4.80457e+04   -4.30776e+04    8.77662e+02    1.96033e+04
1135
    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
1136
    7.90797e+04    9.86830e+04    1.47207e+06    3.03602e+02   -5.41174e+02
1137
   Constr. rmsd
1138
    3.13278e-06
1139

    
1140
           Step           Time
1141
         220000      440.00000
1142

    
1143
   Energies (kJ/mol)
1144
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
1145
    1.20454e+04    6.19527e+04    3.99631e+04    2.31387e+02    5.50874e+03
1146
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
1147
   -1.03446e+04   -4.81696e+04   -4.31943e+04    8.63442e+02    1.88563e+04
1148
    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
1149
    7.93294e+04    9.81857e+04    1.47609e+06    3.04561e+02    4.10618e+02
1150
   Constr. rmsd
1151
    3.07191e-06
1152

    
1153
           Step           Time
1154
         230000      460.00000
1155

    
1156
   Energies (kJ/mol)
1157
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
1158
    1.20581e+04    6.27441e+04    3.99470e+04    2.59537e+02    5.41414e+03
1159
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
1160
   -1.01695e+04   -4.83898e+04   -4.27776e+04    8.66703e+02    1.99526e+04
1161
    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
1162
    7.81974e+04    9.81500e+04    1.47837e+06    3.00215e+02   -2.14167e+02
1163
   Constr. rmsd
1164
    3.05963e-06
1165

    
1166
           Step           Time
1167
         240000      480.00000
1168

    
1169
   Energies (kJ/mol)
1170
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
1171
    1.18368e+04    6.20008e+04    3.99235e+04    2.92633e+02    5.44312e+03
1172
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
1173
   -1.04838e+04   -4.82014e+04   -4.27831e+04    8.53291e+02    1.88820e+04
1174
    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
1175
    7.96486e+04    9.85306e+04    1.48160e+06    3.05787e+02   -9.47722e+01
1176
   Constr. rmsd
1177
    3.04850e-06
1178

    
1179
           Step           Time
1180
         250000      500.00000
1181

    
1182
Writing checkpoint, step 250000 at Fri Feb  2 14:20:03 2018
1183

    
1184

    
1185
   Energies (kJ/mol)
1186
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
1187
    1.19345e+04    6.22533e+04    4.00592e+04    2.56154e+02    5.48456e+03
1188
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
1189
   -1.02050e+04   -4.80708e+04   -4.31039e+04    9.03694e+02    1.95116e+04
1190
    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
1191
    7.90496e+04    9.85613e+04    1.48435e+06    3.03487e+02    3.68526e+02
1192
   Constr. rmsd
1193
    3.16236e-06
1194

    
1195
	<======  ###############  ==>
1196
	<====  A V E R A G E S  ====>
1197
	<==  ###############  ======>
1198

    
1199
	Statistics over 250001 steps using 10001 frames
1200

    
1201
   Energies (kJ/mol)
1202
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
1203
    1.19474e+04    6.18584e+04    3.97869e+04    2.47595e+02    5.39518e+03
1204
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
1205
   -1.02577e+04   -4.84665e+04   -4.27724e+04    8.49401e+02    1.85883e+04
1206
    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
1207
    7.90456e+04    9.76339e+04    9.07775e+05    3.03472e+02    1.17848e+02
1208
   Constr. rmsd
1209
    0.00000e+00
1210

    
1211
          Box-X          Box-Y          Box-Z
1212
    4.80256e+00    4.60917e+00    1.04302e+01
1213

    
1214
   Total Virial (kJ/mol)
1215
    2.37655e+04    2.17659e+02   -4.39822e+02
1216
    2.17626e+02    2.40083e+04    7.13910e+02
1217
   -4.39820e+02    7.13956e+02    2.88199e+04
1218

    
1219
   Pressure (bar)
1220
    1.80067e+01   -1.63318e+01   -1.24132e+00
1221
   -1.63271e+01   -1.02619e+01   -1.09899e+01
1222
   -1.24172e+00   -1.09964e+01    3.45798e+02
1223

    
1224

    
1225
	M E G A - F L O P S   A C C O U N T I N G
1226

    
1227
 NB=Group-cutoff nonbonded kernels    NxN=N-by-N cluster Verlet kernels
1228
 RF=Reaction-Field  VdW=Van der Waals  QSTab=quadratic-spline table
1229
 W3=SPC/TIP3p  W4=TIP4p (single or pairs)
1230
 V&F=Potential and force  V=Potential only  F=Force only
1231

    
1232
 Computing:                               M-Number         M-Flops  % Flops
1233
-----------------------------------------------------------------------------
1234
 Pair Search distance check            3527.403184       31746.629     0.0
1235
 NxN Ewald Elec. + LJ [F]           3431966.005248   267693348.409    92.2
1236
 NxN Ewald Elec. + LJ [V&F]          143033.946624    18451379.114     6.4
1237
 1,4 nonbonded interactions            7721.877218      694968.950     0.2
1238
 Shift-X                                 26.606580         159.639     0.0
1239
 Bonds                                  959.209592       56593.366     0.0
1240
 Propers                               9379.093790     2147812.478     0.7
1241
 Impropers                               28.000280        5824.058     0.0
1242
 Virial                                 319.526625        5751.479     0.0
1243
 Stop-CM                                106.346580        1063.466     0.0
1244
 Calc-Ekin                             1063.253160       28707.835     0.0
1245
 Lincs                                 1681.016810      100861.009     0.0
1246
 Lincs-Mat                            10425.704256       41702.817     0.0
1247
 Constraint-V                          3389.033890       27112.271     0.0
1248
 Constraint-Vir                         204.977080        4919.450     0.0
1249
 Settle                                   9.000090        2907.029     0.0
1250
 Urey-Bradley                          5199.051990      951426.514     0.3
1251
-----------------------------------------------------------------------------
1252
 Total                                               290246284.514   100.0
1253
-----------------------------------------------------------------------------
1254

    
1255

    
1256
     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
1257

    
1258
On 1 MPI rank, each using 24 OpenMP threads
1259

    
1260
 Computing:          Num   Num      Call    Wall time         Giga-Cycles
1261
                     Ranks Threads  Count      (s)         total sum    %
1262
-----------------------------------------------------------------------------
1263
 Neighbor search        1   24       1001       1.880         99.253   1.5
1264
 Launch GPU ops.        1   24     200002      10.567        557.931   8.6
1265
 Force                  1   24     100001      38.104       2011.917  31.0
1266
 Wait PME GPU gather    1   24     100001       7.108        375.324   5.8
1267
 Reduce GPU PME F       1   24     100001       1.555         82.104   1.3
1268
 Wait GPU NB local      1   24     100001      14.731        777.786  12.0
1269
 NB X/F buffer ops.     1   24     199001       5.138        271.311   4.2
1270
 Write traj.            1   24          2       0.091          4.786   0.1
1271
 Update                 1   24     100001       3.614        190.832   2.9
1272
 Constraints            1   24     100001      26.795       1414.770  21.8
1273
 Rest                                          13.192        696.558  10.7
1274
-----------------------------------------------------------------------------
1275
 Total                                        122.776       6482.573 100.0
1276
-----------------------------------------------------------------------------
1277

    
1278
               Core t (s)   Wall t (s)        (%)
1279
       Time:     2946.613      122.776     2400.0
1280
                 (ns/day)    (hour/ns)
1281
Performance:      140.746        0.171
1282
Finished mdrun on rank 0 Fri Feb  2 14:20:03 2018