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md1_ntomp2_ntmpi5_gpu00000.log

Yannic Alber, 07/15/2016 10:48 AM

 
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Log file opened on Thu Jul 14 17:38:06 2016
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Host: falke  pid: 11283  rank ID: 0  number of ranks:  1
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                   :-) GROMACS - gmx mdrun, VERSION 5.1.2 (-:
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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   Sebastian Fritsch 
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  Gerrit Groenhof   Christoph Junghans   Anca Hamuraru    Vincent Hindriksen
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 Dimitrios Karkoulis    Peter Kasson        Jiri Kraus      Carsten Kutzner  
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    Per Larsson      Justin A. Lemkul   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) 2001-2015, 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
24
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 5.1.2
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Executable:   /fasan_w4/shared_soft/gromacs/5.1.2_falke/bin/gmx
30
Data prefix:  /fasan_w4/shared_soft/gromacs/5.1.2_falke
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Command line:
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  gmx mdrun -ntomp 2 -ntmpi 5 -gpu_id 00000 -pin on -s md1.tpr -deffnm md1
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GROMACS version:    VERSION 5.1.2
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Precision:          single
36
Memory model:       64 bit
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MPI library:        thread_mpi
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OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 32)
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GPU support:        enabled
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OpenCL support:     disabled
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invsqrt routine:    gmx_software_invsqrt(x)
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SIMD instructions:  AVX2_256
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FFT library:        fftw-3.3.4-sse2-avx
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RDTSCP usage:       enabled
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C++11 compilation:  disabled
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TNG support:        enabled
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Tracing support:    disabled
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Built on:           Tue Jul 12 15:29:46 CEST 2016
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Built by:           root@falke [CMAKE]
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Build OS/arch:      Linux 4.1.12-1-default x86_64
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Build CPU vendor:   GenuineIntel
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Build CPU brand:    Intel(R) Xeon(R) CPU E5-2640 v4 @ 2.40GHz
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Build CPU family:   6   Model: 79   Stepping: 1
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Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf_lm 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 4.8.5
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C compiler flags:    -march=core-avx2    -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter  -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  -Wno-array-bounds 
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C++ compiler:       /usr/bin/g++ GNU 4.8.5
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C++ compiler flags:  -march=core-avx2    -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function  -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  -Wno-array-bounds 
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Boost version:      1.59.0 (external)
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CUDA compiler:      /local/cuda-8.0/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2016 NVIDIA Corporation;Built on Wed_May__4_21:01:56_CDT_2016;Cuda compilation tools, release 8.0, V8.0.26
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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_52,code=compute_52;-use_fast_math;; ;-march=core-avx2;-Wextra;-Wno-missing-field-initializers;-Wpointer-arith;-Wall;-Wno-unused-function;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;-Wno-array-bounds;
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CUDA driver:        8.0
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CUDA runtime:       8.0
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Running on 1 node with total 20 cores, 20 logical cores, 2 compatible GPUs
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Hardware detected:
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  CPU info:
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    Vendor: GenuineIntel
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    Brand:  Intel(R) Xeon(R) CPU E5-2640 v4 @ 2.40GHz
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    Family:  6  model: 79  stepping:  1
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    CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf_lm 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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    SIMD instructions most likely to fit this hardware: AVX2_256
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    SIMD instructions selected at GROMACS compile time: AVX2_256
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  GPU info:
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    Number of GPUs detected: 2
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    #0: NVIDIA GeForce GTX 1080, compute cap.: 6.1, ECC:  no, stat: compatible
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    #1: NVIDIA GeForce GTX 1080, compute cap.: 6.1, ECC:  no, stat: compatible
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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
84
GROMACS: High performance molecular simulations through multi-level
85
parallelism from laptops to supercomputers
86
SoftwareX 1 (2015) pp. 19-25
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-------- -------- --- Thank You --- -------- --------
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90
++++ 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
93
GROMACS
94
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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Input Parameters:
137
   integrator                     = md
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   tinit                          = 0
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   dt                             = 0.002
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   nsteps                         = 5000000
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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                        = 500
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   bd-fric                        = 0
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   ld-seed                        = 2283639622
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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                        = 5000
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   nstvout                        = 5000
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   nstfout                        = 5000
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   nstlog                         = 5000
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   nstcalcenergy                  = 100
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   nstenergy                      = 5000
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   nstxout-compressed             = 0
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   compressed-x-precision         = 1000
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   cutoff-scheme                  = Verlet
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   nstlist                        = 40
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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        = -1
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   rlist                          = 1.8
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   rlistlong                      = 1.8
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   nstcalclr                      = 40
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   coulombtype                    = PME
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   coulomb-modifier               = Potential-shift
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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                   = Potential-switch
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   rvdw-switch                    = 1
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   rvdw                           = 1.2
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   DispCorr                       = EnerPres
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   table-extension                = 1
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   fourierspacing                 = 0.1
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   fourier-nx                     = 108
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   fourier-ny                     = 108
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   fourier-nz                     = 108
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   pme-order                      = 8
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   ewald-rtol                     = 1e-06
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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                     = 40
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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                     = Isotropic
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   nstpcouple                     = 20
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   tau-p                          = 1
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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                   = TRUE
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   Shake-SOR                      = FALSE
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   shake-tol                      = 0.0001
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   lincs-order                    = 6
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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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   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                    = yes
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   init-lambda                    = -1
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   init-lambda-state              = 1
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   delta-lambda                   = 0
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   nstdhdl                        = 500
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   n-lambdas                      = 11
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   separate-dvdl:
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       fep-lambdas =   FALSE
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      mass-lambdas =   TRUE
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      coul-lambdas =   TRUE
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       vdw-lambdas =   TRUE
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    bonded-lambdas =   TRUE
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 restraint-lambdas =   TRUE
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temperature-lambdas =   FALSE
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all-lambdas:
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       fep-lambdas =            0           0           0           0           0           0           0           0           0           0           0
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      mass-lambdas =            0         0.1         0.2         0.3         0.4         0.5         0.6         0.7         0.8         0.9           1
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      coul-lambdas =            0         0.1         0.2         0.3         0.4         0.5         0.6         0.7         0.8         0.9           1
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       vdw-lambdas =            0         0.1         0.2         0.3         0.4         0.5         0.6         0.7         0.8         0.9           1
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    bonded-lambdas =            0           0           0           0           0           0           0           0           0           0           0
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 restraint-lambdas =            0           0           0           0           0           0           0           0           0           0           0
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temperature-lambdas =            0           0           0           0           0           0           0           0           0           0           0
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   calc-lambda-neighbors          = 1
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   dhdl-print-energy              = no
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   sc-alpha                       = 0
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   sc-power                       = 0
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   sc-r-power                     = 6
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   sc-sigma                       = 0
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   sc-sigma-min                   = 0
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   sc-coul                        = FALSE
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   dh-hist-size                   = 0
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   dh-hist-spacing                = 0.1
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   separate-dhdl-file             = yes
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   dhdl-derivatives               = yes
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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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   E-x:
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      n = 0
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   E-xt:
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      n = 0
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   E-y:
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      n = 0
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   E-yt:
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      n = 0
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   E-z:
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      n = 0
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   E-zt:
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      n = 0
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   swapcoords                     = no
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   adress                         = FALSE
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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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grpopts:
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   nrdf:     14159.8      213180
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   ref-t:         300         300
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   tau-t:         0.1         0.1
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annealing:          No          No
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annealing-npoints:           0           0
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   acc:	           0           0           0
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   nfreeze:           N           N           N
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   energygrp-flags[  0]: 0
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Initializing Domain Decomposition on 5 ranks
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Dynamic load balancing: auto
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Will sort the charge groups at every domain (re)decomposition
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Initial maximum inter charge-group distances:
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    two-body bonded interactions: 0.430 nm, LJ-14, atoms 1224 1231
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  multi-body bonded interactions: 0.430 nm, Proper Dih., atoms 1224 1231
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Minimum cell size due to bonded interactions: 0.473 nm
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Maximum distance for 7 constraints, at 120 deg. angles, all-trans: 0.219 nm
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Estimated maximum distance required for P-LINCS: 0.219 nm
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Using 0 separate PME ranks, per user request
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Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
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Optimizing the DD grid for 5 cells with a minimum initial size of 0.750 nm
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The maximum allowed number of cells is: X 13 Y 13 Z 13
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Domain decomposition grid 5 x 1 x 1, separate PME ranks 0
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PME domain decomposition: 5 x 1 x 1
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Domain decomposition rank 0, coordinates 0 0 0
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Using 5 MPI threads
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Using 2 OpenMP threads per tMPI thread
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1 GPU user-selected for this run.
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Mapping of GPU ID to the 5 PP ranks in this node: 0,0,0,0,0
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NOTE: You assigned GPUs to multiple thread-MPI threads.
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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 ++++
363
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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Will do ordinary reciprocal space Ewald sum.
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Using a Gaussian width (1/beta) of 0.34693 nm for Ewald
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Cut-off's:   NS: 1.8   Coulomb: 1.2   LJ: 1.2
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Long Range LJ corr.: <C6> 2.9922e-04
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System total charge, top. A: 0.000 top. B: 0.000
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Generated table with 1400 data points for Ewald.
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Tabscale = 500 points/nm
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Generated table with 1400 data points for LJ6Switch.
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Tabscale = 500 points/nm
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Generated table with 1400 data points for LJ12Switch.
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Tabscale = 500 points/nm
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Generated table with 1400 data points for 1-4 COUL.
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Tabscale = 500 points/nm
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Generated table with 1400 data points for 1-4 LJ6.
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Tabscale = 500 points/nm
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Generated table with 1400 data points for 1-4 LJ12.
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Tabscale = 500 points/nm
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Potential shift: LJ r^-12: 0.000e+00 r^-6: 0.000e+00, Ewald -1.000e-06
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Initialized non-bonded Ewald correction tables, spacing: 9.71e-04 size: 1237
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Using GPU 8x8 non-bonded kernels
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There are 37 atoms and 37 charges for free energy perturbation
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Pinning threads with an auto-selected logical core stride of 1
393

    
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Initializing Parallel LINear Constraint Solver
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396
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
397
B. Hess
398
P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
399
J. Chem. Theory Comput. 4 (2008) pp. 116-122
400
-------- -------- --- Thank You --- -------- --------
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The number of constraints is 2820
403
There are inter charge-group constraints,
404
will communicate selected coordinates each lincs iteration
405

    
406
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
407
S. Miyamoto and P. A. Kollman
408
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
409
Water Models
410
J. Comp. Chem. 13 (1992) pp. 952-962
411
-------- -------- --- Thank You --- -------- --------
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413

    
414
Linking all bonded interactions to atoms
415

    
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The initial number of communication pulses is: X 1
417
The initial domain decomposition cell size is: X 2.09 nm
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419
The maximum allowed distance for charge groups involved in interactions is:
420
                 non-bonded interactions           1.800 nm
421
(the following are initial values, they could change due to box deformation)
422
            two-body bonded interactions  (-rdd)   1.800 nm
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          multi-body bonded interactions  (-rdd)   1.800 nm
424
  atoms separated by up to 7 constraints  (-rcon)  2.086 nm
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426
When dynamic load balancing gets turned on, these settings will change to:
427
The maximum number of communication pulses is: X 2
428
The minimum size for domain decomposition cells is 1.258 nm
429
The requested allowed shrink of DD cells (option -dds) is: 0.80
430
The allowed shrink of domain decomposition cells is: X 0.60
431
The maximum allowed distance for charge groups involved in interactions is:
432
                 non-bonded interactions           1.800 nm
433
            two-body bonded interactions  (-rdd)   1.800 nm
434
          multi-body bonded interactions  (-rdd)   1.258 nm
435
  atoms separated by up to 7 constraints  (-rcon)  1.258 nm
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438
Making 1D domain decomposition grid 5 x 1 x 1, home cell index 0 0 0
439

    
440
Initial vector of lambda components:[     0.0000     0.1000     0.1000     0.1000     0.0000     0.0000     0.0000 ]
441
Center of mass motion removal mode is Linear
442
We have the following groups for center of mass motion removal:
443
  0:  rest
444

    
445
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
446
G. Bussi, D. Donadio and M. Parrinello
447
Canonical sampling through velocity rescaling
448
J. Chem. Phys. 126 (2007) pp. 014101
449
-------- -------- --- Thank You --- -------- --------
450

    
451
There are: 112248 Atoms
452
Atom distribution over 5 domains: av 22449 stddev 249 min 22245 max 22741
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NOTE: DLB will not turn on during the first phase of PME tuning
455

    
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Initial temperature: 299.324 K
457

    
458
Started mdrun on rank 0 Thu Jul 14 17:38:10 2016
459
           Step           Time         Lambda
460
              0        0.00000        0.00000
461

    
462
   Energies (kJ/mol)
463
           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
464
    4.25857e+03    1.20984e+04    1.48372e+04    6.95575e+02    5.48571e+03
465
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
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    5.82536e+04    2.01087e+05   -5.26742e+03   -1.76704e+06    7.57045e+03
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      Potential    Kinetic En.   Total Energy    Temperature Pres. DC (bar)
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   -1.46802e+06    2.82802e+05   -1.18522e+06    2.99228e+02   -7.71129e+01
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 Pressure (bar)       dEkin/dl      dVcoul/dl       dVvdw/dl    dVbonded/dl
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   -1.51128e+02    3.37730e+01    5.60530e+01    1.61552e+01   -2.10058e+01
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 dVrestraint/dl   Constr. rmsd
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    0.00000e+00    1.49240e-06
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DD  step 39 load imb.: force 282.8%
475

    
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step   80: timed with pme grid 108 108 108, coulomb cutoff 1.200: 4131.1 M-cycles
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step  160: timed with pme grid 100 100 100, coulomb cutoff 1.251: 3993.8 M-cycles
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-------------------------------------------------------
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Program gmx mdrun, VERSION 5.1.2
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Source code file: /fasan_w4/shared_soft/install/gromacs/gromacs-5.1.2/src/gromacs/ewald/pme-redistribute.cpp, line: 276
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Fatal error:
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4 particles communicated to PME rank 1 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
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This usually means that your system is not well equilibrated.
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For more information and tips for troubleshooting, please check the GROMACS
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website at http://www.gromacs.org/Documentation/Errors
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