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membed-2018.log

2018-beta3 - Mark Abraham, 12/26/2017 02:58 PM

 
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Log file opened on Wed Dec 27 00:56:40 2017
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Host: mark-XPS  pid: 22799  rank ID: 0  number of ranks:  1
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                    :-) GROMACS - gmx mdrun, 2018-beta3 (-:
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                            GROMACS is written by:
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     Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par Bjelkmar   
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 Aldert van Buuren   Rudi van Drunen     Anton Feenstra    Gerrit Groenhof  
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 Christoph Junghans   Anca Hamuraru    Vincent Hindriksen Dimitrios Karkoulis
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    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
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  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg   Pieter Meulenhoff 
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   Erik Marklund      Teemu Murtola       Szilard Pall       Sander Pronk   
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   Roland Schulz     Alexey Shvetsov     Michael Shirts     Alfons Sijbers  
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   Peter Tieleman    Teemu Virolainen  Christian Wennberg    Maarten Wolf   
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                           and the project leaders:
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        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
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Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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Copyright (c) 2001-2017, The GROMACS development team at
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Uppsala University, Stockholm University and
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the Royal Institute of Technology, Sweden.
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check out http://www.gromacs.org for more information.
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GROMACS is free software; you can redistribute it and/or modify it
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under the terms of the GNU Lesser General Public License
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as published by the Free Software Foundation; either version 2.1
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of the License, or (at your option) any later version.
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GROMACS:      gmx mdrun, version 2018-beta3
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Executable:   /opt/gromacs/2018-beta3/bin/gmx
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Data prefix:  /opt/gromacs/2018-beta3
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Working dir:  /home/mabraham/redmines/redmine-2364
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Command line:
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  gmx --quiet mdrun -deffnm g_membed -membed embed.dat -mp embedded.top -c embedded.gro
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GROMACS version:    2018-beta3
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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:        disabled
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SIMD instructions:  AVX2_256
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FFT library:        fftw-3.3.6-pl2-sse2-avx
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RDTSCP usage:       enabled
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TNG support:        enabled
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Hwloc support:      hwloc-1.11.0
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Tracing support:    disabled
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Built on:           2017-12-26 13:47:40
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Built by:           mabraham@mark-XPS [CMAKE]
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Build OS/arch:      Linux 4.13.0-19-generic x86_64
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Build CPU vendor:   Intel
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Build CPU brand:    Intel(R) Core(TM) i7-7500U CPU @ 2.70GHz
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Build CPU family:   6   Model: 142   Stepping: 9
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Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
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C compiler:         /usr/bin/gcc GNU 7.2.0
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C compiler flags:    -march=core-avx2    -Wundef -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter  -O3  -funroll-all-loops -fexcess-precision=fast  
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C++ compiler:       /usr/bin/g++ GNU 7.2.0
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C++ compiler flags:  -march=core-avx2    -std=c++11  -Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wmissing-declarations -Wall  -O3  -funroll-all-loops -fexcess-precision=fast  
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Running on 1 node with total 2 cores, 4 logical cores
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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) Core(TM) i7-7500U CPU @ 2.70GHz
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    Family: 6   Model: 142   Stepping: 9
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    Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp 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   2] [   1   3]
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    Numa nodes:
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      Node  0 (8246362112 bytes mem):   0   1   2   3
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      Latency:
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               0
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         0  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. 4, shared 2 ways
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      L3: 4194304 bytes, linesize 64 bytes, assoc. 16, shared 4 ways
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    PCI devices:
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      0000:00:02.0  Id: 8086:5916  Class: 0x0300  Numa: 0
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      0000:3a:00.0  Id: 168c:003e  Class: 0x0280  Numa: 0
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      0000:3c:00.0  Id: 1c5c:1283  Class: 0x0108  Numa: 0
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
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Lindahl
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GROMACS: High performance molecular simulations through multi-level
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parallelism from laptops to supercomputers
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SoftwareX 1 (2015) pp. 19-25
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
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Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
97
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
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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
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-------- -------- --- 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
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molecular simulation
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J. Chem. Theory Comput. 4 (2008) pp. 435-447
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-------- -------- --- 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
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-------- -------- --- Thank You --- -------- --------
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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
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J. Mol. Mod. 7 (2001) pp. 306-317
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-------- -------- --- Thank You --- -------- --------
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++++ 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
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Comp. Phys. Comm. 91 (1995) pp. 43-56
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-------- -------- --- Thank You --- -------- --------
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Membrane embedding only supports a single rank. Choosing to use only a single thread-MPI rank.
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Input Parameters:
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   integrator                     = md
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   tinit                          = 0
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   dt                             = 0.002
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   nsteps                         = 1000
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   init-step                      = 0
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   simulation-part                = 1
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   comm-mode                      = Linear
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   nstcomm                        = 100
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   bd-fric                        = 0
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   ld-seed                        = -1006645558
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   emtol                          = 10
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   emstep                         = 0.01
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   niter                          = 20
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   fcstep                         = 0
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   nstcgsteep                     = 1000
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   nbfgscorr                      = 10
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   rtpi                           = 0.05
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   nstxout                        = 0
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   nstvout                        = 0
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   nstfout                        = 0
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   nstlog                         = 1000
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   nstcalcenergy                  = 100
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   nstenergy                      = 100
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   nstxout-compressed             = 1000
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   compressed-x-precision         = 1000
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   cutoff-scheme                  = Group
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   nstlist                        = 10
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   ns-type                        = Grid
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   pbc                            = xyz
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   periodic-molecules             = false
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   verlet-buffer-tolerance        = 0.005
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   rlist                          = 1.2
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   coulombtype                    = PME
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   coulomb-modifier               = None
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   rcoulomb-switch                = 0
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   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                    = 0.8
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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                     = 72
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   fourier-ny                     = 72
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   fourier-nz                     = 80
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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
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   epsilon-surface                = 0
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   implicit-solvent               = No
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   gb-algorithm                   = Still
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   nstgbradii                     = 1
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   rgbradii                       = 1
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   gb-epsilon-solvent             = 80
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   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
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   sa-surface-tension             = 2.05016
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   tcoupl                         = V-rescale
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   nsttcouple                     = 10
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   nh-chain-length                = 0
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   print-nose-hoover-chain-variables = false
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   pcoupl                         = Berendsen
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   pcoupltype                     = Semiisotropic
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   nstpcouple                     = 10
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   tau-p                          = 5
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   compressibility (3x3):
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      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,  4.50000e-05}
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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               = No
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   posres-com (3):
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      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
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   QMconstraints                  = 0
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   QMMMscheme                     = 0
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   MMChargeScaleFactor            = 1
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qm-opts:
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   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                    = 8
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   lincs-iter                     = 2
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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                           = false
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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:
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   nrdf:       63997       63045           0
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   ref-t:         298         298         298
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   tau-t:         0.1         0.1         0.1
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annealing:          No          No          No
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annealing-npoints:           0           0           0
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   acc:	           0           0           0
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   nfreeze:           Y           Y           Y           N           N           N
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   energygrp-flags[  0]: 1 0
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   energygrp-flags[  1]: 0 0
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Using 1 MPI thread
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Pinning threads with an auto-selected logical core stride of 2
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rm mol 102
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rm mol 147
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rm mol 108
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rm mol 144
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rm mol 71
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rm mol 49
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rm mol 69
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rm mol 1805
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rm mol 328
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rm mol 9392
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rm mol 2284
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rm mol 10152
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rm mol 1789
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rm mol 6832
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rm mol 7395
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rm mol 79
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rm mol 34
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rm mol 7972
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rm mol 4029
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rm mol 1871
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rm mol 9661
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rm mol 2699
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rm mol 10279
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rm mol 3550
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rm mol 2821
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rm mol 4338
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rm mol 141
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rm mol 2063
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rm mol 6289
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rm mol 848
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rm mol 10575
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rm mol 2658
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rm mol 146
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rm mol 5426
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rm mol 1181
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rm mol 2195
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rm mol 2204
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rm mol 5726
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rm mol 149
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rm mol 1855
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rm mol 1571
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rm mol 5
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rm mol 21
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rm mol 65
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rm mol 14
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rm mol 42
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rm mol 81
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rm mol 22
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rm mol 91
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rm mol 64
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rm mol 84
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rm mol 12
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rm mol 54
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NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be
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removed in a future release when 'verlet' supports all interaction forms.
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System total charge: 4.000
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Will do PME sum in reciprocal space for electrostatic interactions.
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
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A smooth particle mesh Ewald method
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J. Chem. Phys. 103 (1995) pp. 8577-8592
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-------- -------- --- Thank You --- -------- --------
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Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
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Potential shift: LJ r^-12: -4.985e-01 r^-6: -8.000e-01, Ewald -0.000e+00
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Initialized non-bonded Ewald correction tables, spacing: 1.02e-03 size: 2154
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Table routines are used for coulomb: false
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Table routines are used for vdw:     false
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Cut-off's:   NS: 1.2   Coulomb: 1.2   LJ: 1.2
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Generated table with 1100 data points for 1-4 COUL.
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Tabscale = 500 points/nm
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Generated table with 1100 data points for 1-4 LJ6.
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Tabscale = 500 points/nm
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Generated table with 1100 data points for 1-4 LJ12.
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Tabscale = 500 points/nm
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Removing pbc first time
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Initializing LINear Constraint Solver
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
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LINCS: A Linear Constraint Solver for molecular simulations
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J. Comp. Chem. 18 (1997) pp. 1463-1472
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-------- -------- --- Thank You --- -------- --------
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The number of constraints is 14432
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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S. Miyamoto and P. A. Kollman
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SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
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Water Models
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J. Comp. Chem. 13 (1992) pp. 952-962
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-------- -------- --- Thank You --- -------- --------
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Intra-simulation communication will occur every 10 steps.
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Center of mass motion removal mode is Linear
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We have the following groups for center of mass motion removal:
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  0:  Other
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  1:  Water_and_ions
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  2:  Protein
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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G. Bussi, D. Donadio and M. Parrinello
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Canonical sampling through velocity rescaling
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J. Chem. Phys. 126 (2007) pp. 014101
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-------- -------- --- Thank You --- -------- --------
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There are: 60872 Atoms
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Constraining the starting coordinates (step 0)
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Constraining the coordinates at t0-dt (step 0)
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RMS relative constraint deviation after constraining: 1.09e-06
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Initial temperature: 447.309 K
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Started mdrun on rank 0 Wed Dec 27 00:56:44 2017
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           Step           Time
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              0        0.00000
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Note: The available nonbonded kernels do not support water optimization - disabling.
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Grid: 15 x 15 x 18 cells
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   Energies (kJ/mol)
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           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
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    1.00225e+04    5.69853e+04    3.80606e+04    4.21643e+02    5.89257e+03
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     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
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   -8.52978e+04    1.29589e+06   -3.54771e+05   -2.45597e+05    7.21604e+05
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    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
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           -nan           -nan           -nan           -nan           -nan
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   Constr. rmsd
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    1.09817e-06
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