GROMACS

                      :-) GROMACS - gmx mdrun, 2019.1 (-:

                            GROMACS is written by:

     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen

    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    

 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     

  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  

  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis

    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    

  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   

    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   

    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  

   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 

 Christian Wennberg    Maarten Wolf   

                           and the project leaders:

        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.

Copyright (c) 2001-2018, The GROMACS development team at

Uppsala University, Stockholm University and

the Royal Institute of Technology, Sweden.

check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it

under the terms of the GNU Lesser General Public License

as published by the Free Software Foundation; either version 2.1

of the License, or (at your option) any later version.

GROMACS:      gmx mdrun, version 2019.1

Executable:   /apps/broadwell/centos7/GROMACS/2019.1-intel-2018b-UArecipe/bin/gmx_mpi

Data prefix:  /apps/broadwell/centos7/GROMACS/2019.1-intel-2018b-UArecipe

Working dir:  /scratch/gromacs-2019/test2019

Process ID:   22580

Command line:

  gmx_mpi mdrun -ntomp 1 -s 0519.tpr -o /scratch/gromacs-2019/test2019/0519.trr -x /scratch/gromacs-2019/test2019/0519.xtc -cpo /scratch/gromacs-2019/test2019/0519.cpt -c /scratch/gromacs-2019/test2019/0519.gro -e /scratch/gromacs-2019/test2019/0519.edr -dhdl /scratch/gromacs-2019/test2019/0519.xvg -g /scratch/gromacs-2019/test2019/0519.log -px /scratch/gromacs-2019/test2019/0519.x.xvg -pf /scratch/gromacs-2019/test2019/0519.f.xvg -noconfout -rcon 0.7 -pin on -dds 0.9 -dlb auto -maxh 1

GROMACS version:    2019.1

Precision:          single

Memory model:       64 bit

MPI library:        MPI

OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)

GPU support:        disabled

SIMD instructions:  AVX2_256

FFT library:        Intel MKL

RDTSCP usage:       enabled

TNG support:        enabled

Hwloc support:      hwloc-1.11.8

Tracing support:    disabled

C compiler:         /apps/noarch/intel-psxe/2018_update3/compilers_and_libraries_2018.3.222/linux/mpi/intel64/bin/mpiicc Intel 18.0.3.20180410

C compiler flags:    -march=core-avx2   -mkl=sequential  -std=gnu99  -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits  

C++ compiler:       /apps/noarch/intel-psxe/2018_update3/compilers_and_libraries_2018.3.222/linux/mpi/intel64/bin/mpiicpc Intel 18.0.3.20180410

C++ compiler flags:  -march=core-avx2   -mkl=sequential  -std=c++11   -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits  

Running on 4 nodes with total 112 cores, 112 logical cores

  Cores per node:           28

  Logical cores per node:   28

Hardware detected on host r1c04cn1.leibniz (the node of MPI rank 0):

  CPU info:

    Vendor: Intel

    Brand:  Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz

    Family: 6   Model: 79   Stepping: 1

    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

  Hardware topology: Full, with devices

    Sockets, cores, and logical processors:

      Socket  0: [   0] [   1] [   2] [   3] [   4] [   5] [   6] [   7] [   8] [   9] [  10] [  11] [  12] [  13]

      Socket  1: [  14] [  15] [  16] [  17] [  18] [  19] [  20] [  21] [  22] [  23] [  24] [  25] [  26] [  27]

    Numa nodes:

      Node  0 (68600541184 bytes mem):   0   1   2   3   4   5   6   7   8   9  10  11  12  13

      Node  1 (68719476736 bytes mem):  14  15  16  17  18  19  20  21  22  23  24  25  26  27

      Latency:

               0     1

         0  1.00  2.10

         1  2.10  1.00

    Caches:

      L1: 32768 bytes, linesize 64 bytes, assoc. 8, shared 1 ways

      L2: 262144 bytes, linesize 64 bytes, assoc. 8, shared 1 ways

      L3: 36700160 bytes, linesize 64 bytes, assoc. 20, shared 14 ways

    PCI devices:

      0000:01:00.0  Id: 8086:1521  Class: 0x0200  Numa: 0

      0000:01:00.1  Id: 8086:1521  Class: 0x0200  Numa: 0

      0000:02:00.0  Id: 15b3:1013  Class: 0x0207  Numa: 0

      0000:00:11.4  Id: 8086:8d62  Class: 0x0106  Numa: 0

      0000:07:00.0  Id: 1a03:2000  Class: 0x0300  Numa: 0

      0000:00:1f.2  Id: 8086:8d02  Class: 0x0106  Numa: 0

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++

M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.

Lindahl

GROMACS: High performance molecular simulations through multi-level

parallelism from laptops to supercomputers

SoftwareX 1 (2015) pp. 19-25

-------- -------- --- Thank You --- -------- --------

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++

S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl

Tackling Exascale Software Challenges in Molecular Dynamics Simulations with

GROMACS

In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27

-------- -------- --- Thank You --- -------- --------

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++

S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.

Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl

GROMACS 4.5: a high-throughput and highly parallel open source molecular

simulation toolkit

Bioinformatics 29 (2013) pp. 845-54

-------- -------- --- Thank You --- -------- --------

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++

B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl

GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable

molecular simulation

J. Chem. Theory Comput. 4 (2008) pp. 435-447

-------- -------- --- Thank You --- -------- --------

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++

D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.

Berendsen

GROMACS: Fast, Flexible and Free

J. Comp. Chem. 26 (2005) pp. 1701-1719

-------- -------- --- Thank You --- -------- --------

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++

E. Lindahl and B. Hess and D. van der Spoel

GROMACS 3.0: A package for molecular simulation and trajectory analysis

J. Mol. Mod. 7 (2001) pp. 306-317

-------- -------- --- Thank You --- -------- --------

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++

H. J. C. Berendsen, D. van der Spoel and R. van Drunen

GROMACS: A message-passing parallel molecular dynamics implementation

Comp. Phys. Comm. 91 (1995) pp. 43-56

-------- -------- --- Thank You --- -------- --------

++++ PLEASE CITE THE DOI FOR THIS VERSION OF GROMACS ++++

https://doi.org/10.5281/zenodo.2564764

-------- -------- --- Thank You --- -------- --------

Input Parameters:

   integrator                     = md

   tinit                          = 0

   dt                             = 0.002

   nsteps                         = 500000

   init-step                      = 0

   simulation-part                = 1

   comm-mode                      = Linear

   nstcomm                        = 100

   bd-fric                        = 0

   ld-seed                        = -1437393019

   emtol                          = 10

   emstep                         = 0.01

   niter                          = 20

   fcstep                         = 0

   nstcgsteep                     = 1000

   nbfgscorr                      = 10

   rtpi                           = 0.05

   nstxout                        = 0

   nstvout                        = 0

   nstfout                        = 0

   nstlog                         = 50000

   nstcalcenergy                  = 100

   nstenergy                      = 50000

   nstxout-compressed             = 50000

   compressed-x-precision         = 1000

   cutoff-scheme                  = Verlet

   nstlist                        = 20

   ns-type                        = Grid

   pbc                            = xyz

   periodic-molecules             = false

   verlet-buffer-tolerance        = 0.005

   rlist                          = 1.223

   coulombtype                    = PME

   coulomb-modifier               = Potential-shift

   rcoulomb-switch                = 0

   rcoulomb                       = 1.2

   epsilon-r                      = 1

   epsilon-rf                     = inf

   vdw-type                       = Cut-off

   vdw-modifier                   = Potential-shift

   rvdw-switch                    = 1

   rvdw                           = 1.2

   DispCorr                       = EnerPres

   table-extension                = 1

   fourierspacing                 = 0.16

   fourier-nx                     = 96

   fourier-ny                     = 84

   fourier-nz                     = 80

   pme-order                      = 4

   ewald-rtol                     = 1e-05

   ewald-rtol-lj                  = 0.001

   lj-pme-comb-rule               = Geometric

   ewald-geometry                 = 0

   epsilon-surface                = 0

   tcoupl                         = V-rescale

   nsttcouple                     = 20

   nh-chain-length                = 0

   print-nose-hoover-chain-variables = false

   pcoupl                         = Berendsen

   pcoupltype                     = Isotropic

   nstpcouple                     = 20

   tau-p                          = 2

   compressibility (3x3):

      compressibility[    0]={ 4.50000e-05,  0.00000e+00,  0.00000e+00}

      compressibility[    1]={ 0.00000e+00,  4.50000e-05,  0.00000e+00}

      compressibility[    2]={ 0.00000e+00,  0.00000e+00,  4.50000e-05}

   ref-p (3x3):

      ref-p[    0]={ 1.00000e+00,  0.00000e+00,  0.00000e+00}

      ref-p[    1]={ 0.00000e+00,  1.00000e+00,  0.00000e+00}

      ref-p[    2]={ 0.00000e+00,  0.00000e+00,  1.00000e+00}

   refcoord-scaling               = COM

   posres-com (3):

      posres-com[0]= 0.00000e+00

      posres-com[1]= 0.00000e+00

      posres-com[2]= 0.00000e+00

   posres-comB (3):

      posres-comB[0]= 0.00000e+00

      posres-comB[1]= 0.00000e+00

      posres-comB[2]= 0.00000e+00

   QMMM                           = false

   QMconstraints                  = 0

   QMMMscheme                     = 0

   MMChargeScaleFactor            = 1

qm-opts:

   ngQM                           = 0

   constraint-algorithm           = Lincs

   continuation                   = true

   Shake-SOR                      = false

   shake-tol                      = 0.0001

   lincs-order                    = 4

   lincs-iter                     = 1

   lincs-warnangle                = 30

   nwall                          = 0

   wall-type                      = 9-3

   wall-r-linpot                  = -1

   wall-atomtype[0]               = -1

   wall-atomtype[1]               = -1

   wall-density[0]                = 0

   wall-density[1]                = 0

   wall-ewald-zfac                = 3

   pull                           = true

   pull-cylinder-r                = 1.5

   pull-constr-tol                = 1e-06

   pull-print-COM                 = true

   pull-print-ref-value           = true

   pull-print-components          = true

   pull-nstxout                   = 50000

   pull-nstfout                   = 50000

   pull-pbc-ref-prev-step-com     = false

   pull-xout-average              = false

   pull-fout-average              = false

   pull-ngroups                   = 3

   pull-group 0:

     atom: not available

     weight: not available

     pbcatom                        = -1

   pull-group 1:

     atom (1):

        atom[0]=1442

     weight: not available

     pbcatom                        = -1

   pull-group 2:

     atom (2):

        atom[0]=4641

        atom[1]=4643

     weight: not available

     pbcatom                        = 4641

   pull-ncoords                   = 1

   pull-coord 0:

   type                           = umbrella

   geometry                       = distance

   group[0]                       = 1

   group[1]                       = 2

   dim (3):

      dim[0]=1

      dim[1]=1

      dim[2]=1

   origin (3):

      origin[0]= 0.00000e+00

      origin[1]= 0.00000e+00

      origin[2]= 0.00000e+00

   vec (3):

      vec[0]= 0.00000e+00

      vec[1]= 0.00000e+00

      vec[2]= 0.00000e+00

   start                          = true

   init                           = 0.518654

   rate                           = 0

   k                              = 1000

   kB                             = 1000

   awh                            = false

   rotation                       = false

   interactiveMD                  = false

   disre                          = No

   disre-weighting                = Conservative

   disre-mixed                    = false

   dr-fc                          = 1000

   dr-tau                         = 0

   nstdisreout                    = 100

   orire-fc                       = 0

   orire-tau                      = 0

   nstorireout                    = 100

   free-energy                    = no

   cos-acceleration               = 0

   deform (3x3):

      deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}

      deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}

      deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}

   simulated-tempering            = false

   swapcoords                     = no

   userint1                       = 0

   userint2                       = 0

   userint3                       = 0

   userint4                       = 0

   userreal1                      = 0

   userreal2                      = 0

   userreal3                      = 0

   userreal4                      = 0

   applied-forces:

     electric-field:

       x:

         E0                       = 0

         omega                    = 0

         t0                       = 0

         sigma                    = 0

       y:

         E0                       = 0

         omega                    = 0

         t0                       = 0

         sigma                    = 0

       z:

         E0                       = 0

         omega                    = 0

         t0                       = 0

         sigma                    = 0

grpopts:

   nrdf:     12909.9      439152

   ref-t:         300         300

   tau-t:         0.1         0.1

annealing:          No          No

annealing-npoints:           0           0

   acc:	           0           0           0

   nfreeze:           N           N           N

   energygrp-flags[  0]: 0

Changing nstlist from 20 to 80, rlist from 1.223 to 1.326

Initializing Domain Decomposition on 112 ranks

Dynamic load balancing: locked

Using update groups, nr 76781, average size 2.9 atoms, max. radius 0.125 nm

Minimum cell size due to atom displacement: 0.514 nm

Initial maximum distances in bonded interactions:

    two-body bonded interactions: 0.443 nm, LJ-14, atoms 1990 2780

  multi-body bonded interactions: 0.443 nm, Proper Dih., atoms 1990 2780

Minimum cell size due to bonded interactions: 0.487 nm

User supplied maximum distance required for P-LINCS: 0.700 nm

Guess for relative PME load: 0.13

Will use 96 particle-particle and 16 PME only ranks

This is a guess, check the performance at the end of the log file

Using 16 separate PME ranks, as guessed by mdrun

Scaling the initial minimum size with 1/0.9 (option -dds) = 1.11111

Optimizing the DD grid for 96 cells with a minimum initial size of 0.778 nm

The maximum allowed number of cells is: X 18 Y 17 Z 15

Domain decomposition grid 4 x 4 x 6, separate PME ranks 16

PME domain decomposition: 4 x 4 x 1

Interleaving PP and PME ranks

This rank does only particle-particle work.

Domain decomposition rank 0, coordinates 0 0 0

The initial number of communication pulses is: X 1 Y 1 Z 1

The initial domain decomposition cell size is: X 3.63 nm Y 3.31 nm Z 2.00 nm

The maximum allowed distance for atom groups involved in interactions is:

                 non-bonded interactions           1.576 nm

(the following are initial values, they could change due to box deformation)

            two-body bonded interactions  (-rdd)   1.576 nm

          multi-body bonded interactions  (-rdd)   1.576 nm

When dynamic load balancing gets turned on, these settings will change to:

The maximum number of communication pulses is: X 1 Y 1 Z 1

The minimum size for domain decomposition cells is 1.576 nm

The requested allowed shrink of DD cells (option -dds) is: 0.90

The allowed shrink of domain decomposition cells is: X 0.43 Y 0.48 Z 0.79

The maximum allowed distance for atom groups involved in interactions is:

                 non-bonded interactions           1.576 nm

            two-body bonded interactions  (-rdd)   1.576 nm

          multi-body bonded interactions  (-rdd)   1.576 nm

Using two step summing over 4 groups of on average 24.0 ranks

Using 112 MPI processes

Using 1 OpenMP thread per MPI process

Overriding thread affinity set outside gmx mdrun

Pinning threads with an auto-selected logical core stride of 1

System total charge: -0.000

Will do PME sum in reciprocal space for electrostatic interactions.

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++

U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 

A smooth particle mesh Ewald method

J. Chem. Phys. 103 (1995) pp. 8577-8592

-------- -------- --- Thank You --- -------- --------

Using a Gaussian width (1/beta) of 0.384195 nm for Ewald

Potential shift: LJ r^-12: -1.122e-01 r^-6: -3.349e-01, Ewald -8.333e-06

Initialized non-bonded Ewald correction tables, spacing: 1.02e-03 size: 1176

Long Range LJ corr.: <C6> 3.1361e-04

Generated table with 1163 data points for Ewald.

Tabscale = 500 points/nm

Generated table with 1163 data points for LJ6.

Tabscale = 500 points/nm

Generated table with 1163 data points for LJ12.

Tabscale = 500 points/nm

Generated table with 1163 data points for 1-4 COUL.

Tabscale = 500 points/nm

Generated table with 1163 data points for 1-4 LJ6.

Tabscale = 500 points/nm

Generated table with 1163 data points for 1-4 LJ12.

Tabscale = 500 points/nm

Using SIMD 4x8 nonbonded short-range kernels

Using a dual 4x8 pair-list setup updated with dynamic pruning:

  outer list: updated every 80 steps, buffer 0.126 nm, rlist 1.326 nm

  inner list: updated every 13 steps, buffer 0.002 nm, rlist 1.202 nm

At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:

  outer list: updated every 80 steps, buffer 0.275 nm, rlist 1.475 nm

  inner list: updated every 13 steps, buffer 0.052 nm, rlist 1.252 nm

Using full Lennard-Jones parameter combination matrix

Will apply potential COM pulling

with 1 pull coordinate and 2 groups

Pull group 1:     1 atoms, mass    13.019

Pull group 2:     2 atoms, mass    26.018

Will use a sub-communicator for pull communication

Initializing LINear Constraint Solver

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++

B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije

LINCS: A Linear Constraint Solver for molecular simulations

J. Comp. Chem. 18 (1997) pp. 1463-1472

-------- -------- --- Thank You --- -------- --------

The number of constraints is 1073

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++

S. Miyamoto and P. A. Kollman

SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid

Water Models

J. Comp. Chem. 13 (1992) pp. 952-962

-------- -------- --- Thank You --- -------- --------

Linking all bonded interactions to atoms

The -noconfout functionality is deprecated, and may be removed in a future version.

Intra-simulation communication will occur every 20 steps.

Center of mass motion removal mode is Linear

We have the following groups for center of mass motion removal:

  0:  rest

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++

G. Bussi, D. Donadio and M. Parrinello

Canonical sampling through velocity rescaling

J. Chem. Phys. 126 (2007) pp. 014101

-------- -------- --- Thank You --- -------- --------