This is all the log file.
:-) GROMACS - gmx mdrun, 2022.2-dev (-:
Copyright 1991-2022 The GROMACS Authors.
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.
Current GROMACS contributors:
Mark Abraham Andrey Alekseenko Cathrine Bergh
Christian Blau Eliane Briand Kevin Boyd
Oliver Fleetwood Stefan Fleischmann Vytas Gapsys
Gaurav Garg Gilles Gouaillardet Alan Gray
Victor Holanda M. Eric Irrgang Joe Jordan
Christoph Junghans Prashanth Kanduri Sebastian Kehl
Sebastian Keller Carsten Kutzner Magnus Lundborg
Pascal Merz Dmitry Morozov Szilard Pall
Roland Schulz Michael Shirts David van der Spoel
Alessandra Villa Sebastian Wingbermuehle Artem Zhmurov
Previous GROMACS contributors:
Emile Apol Rossen Apostolov James Barnett
Herman J.C. Berendsen Par Bjelkmar Viacheslav Bolnykh
Aldert van Buuren Carlo Camilloni Rudi van Drunen
Anton Feenstra Gerrit Groenhof Bert de Groot
Anca Hamuraru Vincent Hindriksen Aleksei Iupinov
Dimitrios Karkoulis Peter Kasson Jiri Kraus
Per Larsson Justin A. Lemkul Viveca Lindahl
Erik Marklund Pieter Meulenhoff Vedran Miletic
Teemu Murtola Sander Pronk Alexey Shvetsov
Alfons Sijbers Peter Tieleman Jon Vincent
Teemu Virolainen Christian Wennberg Maarten Wolf
Coordinated by the GROMACS project leaders:
Paul Bauer, Berk Hess, and Erik Lindahl
GROMACS: gmx mdrun, version 2022.2-dev
Executable: /es01/paratera/parasoft/gromacs-2022.2/install/bin/gmx_mpi
Data prefix: /es01/paratera/parasoft/gromacs-2022.2/install
Working dir: /es01/paratera/sce2008/4RMH
Process ID: 181180
Command line:
gmx_mpi mdrun -deffnm md_0_10
GROMACS version: 2022.2-dev
Precision: mixed
Memory model: 64 bit
MPI library: MPI
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 128)
GPU support: disabled
SIMD instructions: AVX2_256
CPU FFT library: fftw-3.3.8-sse2-avx-avx2-avx2_128
GPU FFT library: none
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: disabled
Tracing support: disabled
C compiler: /es01/software/intel2020/compilers_and_libraries_2020.4.304/linux/mpi/intel64/bin/mpicc GNU 8.3.0
C compiler flags: -mavx2 -mfma -Wall -Wno-unused -Wunused-value -Wunused-parameter -Wextra -Wno-sign-compare -Wpointer-arith -Wundef -Werror=stringop-truncation -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-array-bounds -O3 -DNDEBUG
C++ compiler: /es01/software/intel2020/compilers_and_libraries_2020.4.304/linux/mpi/intel64/bin/mpicxx GNU 8.3.0
C++ compiler flags: -mavx2 -mfma -Wall -Wextra -Wpointer-arith -Wmissing-declarations -Wundef -Wstringop-truncation -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-array-bounds -fopenmp -O3 -DNDEBUG
Running on 1 node with total 56 cores, 56 processing units
Hardware detected on host n02318 (the node of MPI rank 0):
CPU info:
Vendor: Intel
Brand: Intel(R) Xeon(R) Gold 6258R CPU @ 2.70GHz
Family: 6 Model: 85 Stepping: 7
Features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl avx512secondFMA 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
Number of AVX-512 FMA units: 2
Hardware topology: Basic
Packages, cores, and logical processors:
[indices refer to OS logical processors]
Package 0: [ 0] [ 1] [ 2] [ 3] [ 4] [ 5] [ 6] [ 7] [ 8] [ 9] [ 10] [ 11] [ 12] [ 13] [ 14] [ 15] [ 16] [ 17] [ 18] [ 19] [ 20] [ 21] [ 22] [ 23] [ 24] [ 25] [ 26] [ 27]
Package 1: [ 28] [ 29] [ 30] [ 31] [ 32] [ 33] [ 34] [ 35] [ 36] [ 37] [ 38] [ 39] [ 40] [ 41] [ 42] [ 43] [ 44] [ 45] [ 46] [ 47] [ 48] [ 49] [ 50] [ 51] [ 52] [ 53] [ 54] [ 55]
CPU limit set by OS: -1 Recommended max number of threads: 56
Highest SIMD level supported by all nodes in run: AVX_512
SIMD instructions selected at compile time: AVX2_256
This program was compiled for different hardware than you are running on,
which could influence performance. This build might have been configured on a
login node with only a single AVX-512 FMA unit (in which case AVX2 is faster),
while the node you are running on has dual AVX-512 FMA units.
++++ 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 ++++
-------- -------- — Thank You — -------- --------
Input Parameters:
integrator = md
tinit = 0
dt = 0.002
nsteps = 5000000
init-step = 0
simulation-part = 1
mts = false
comm-mode = Linear
nstcomm = 100
bd-fric = 0
ld-seed = 2006896589
emtol = 10
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
rtpi = 0.05
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 5000
nstcalcenergy = 100
nstenergy = 5000
nstxout-compressed = 5000
compressed-x-precision = 1000
cutoff-scheme = Verlet
nstlist = 20
pbc = xyz
periodic-molecules = false
verlet-buffer-tolerance = 0.005
rlist = 1.222
coulombtype = PME
coulomb-modifier = Potential-shift
rcoulomb-switch = 0
rcoulomb = 1.2
epsilon-r = 1
epsilon-rf = inf
vdw-type = Cut-off
vdw-modifier = Force-switch
rvdw-switch = 1
rvdw = 1.2
DispCorr = No
table-extension = 1
fourierspacing = 0.16
fourier-nx = 56
fourier-ny = 56
fourier-nz = 56
pme-order = 4
ewald-rtol = 1e-05
ewald-rtol-lj = 0.001
lj-pme-comb-rule = Geometric
ewald-geometry = 3d
epsilon-surface = 0
tcoupl = V-rescale
nsttcouple = 10
nh-chain-length = 0
print-nose-hoover-chain-variables = false
pcoupl = Parrinello-Rahman
pcoupltype = Isotropic
nstpcouple = 10
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 = No
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
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 = false
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
density-guided-simulation:
active = false
group = protein
similarity-measure = inner-product
atom-spreading-weight = unity
force-constant = 1e+09
gaussian-transform-spreading-width = 0.2
gaussian-transform-spreading-range-in-multiples-of-width = 4
reference-density-filename = reference.mrc
nst = 1
normalize-densities = true
adaptive-force-scaling = false
adaptive-force-scaling-time-constant = 4
shift-vector =
transformation-matrix =
qmmm-cp2k:
active = false
qmgroup = System
qmmethod = PBE
qmfilenames =
qmcharge = 0
qmmultiplicity = 1
grpopts:
nrdf: 11739.7 93939.3
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 1.222 to 1.319
When checking whether update groups are usable:
At least one moleculetype does not conform to the requirements for using update groups
Initializing Domain Decomposition on 56 ranks
Dynamic load balancing: auto
Minimum cell size due to atom displacement: 0.644 nm
Initial maximum distances in bonded interactions:
two-body bonded interactions: 0.433 nm, LJ-14, atoms 3256 3264
multi-body bonded interactions: 0.495 nm, CMAP Dih., atoms 3842 3851
Minimum cell size due to bonded interactions: 0.545 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.222 nm
Estimated maximum distance required for P-LINCS: 0.222 nm
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Guess for relative PME load: 0.12
Will use 49 particle-particle and 7 PME only ranks
This is a guess, check the performance at the end of the log file
Using 7 separate PME ranks, as guessed by mdrun
Optimizing the DD grid for 49 cells with a minimum initial size of 0.805 nm
The maximum allowed number of cells is: X 9 Y 9 Z 7
Domain decomposition grid 7 x 7 x 1, separate PME ranks 7
PME domain decomposition: 7 x 1 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 2 Y 2
The initial domain decomposition cell size is: X 1.04 nm Y 1.04 nm
The maximum allowed distance for atoms involved in interactions is:
non-bonded interactions 1.319 nm
(the following are initial values, they could change due to box deformation)
two-body bonded interactions (-rdd) 1.319 nm
multi-body bonded interactions (-rdd) 1.044 nm
atoms separated by up to 5 constraints (-rcon) 1.044 nm
When dynamic load balancing gets turned on, these settings will change to:
The maximum number of communication pulses is: X 2 Y 2
The minimum size for domain decomposition cells is 0.794 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: X 0.76 Y 0.76
The maximum allowed distance for atoms involved in interactions is:
non-bonded interactions 1.319 nm
two-body bonded interactions (-rdd) 1.319 nm
multi-body bonded interactions (-rdd) 0.794 nm
atoms separated by up to 5 constraints (-rcon) 0.794 nm
Using 56 MPI processes
Non-default thread affinity set, disabling internal thread affinity
Using 1 OpenMP thread per MPI process
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: -2.648e-01 r^-6: -5.349e-01, Ewald -8.333e-06
Initialized non-bonded Coulomb Ewald tables, spacing: 1.02e-03 size: 1176
Generated table with 1159 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1159 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1159 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 0.119 nm, rlist 1.319 nm
inner list: updated every 13 steps, buffer 0.001 nm, rlist 1.201 nm
At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
outer list: updated every 80 steps, buffer 0.263 nm, rlist 1.463 nm
inner list: updated every 13 steps, buffer 0.051 nm, rlist 1.251 nm
Linking all bonded interactions to atoms
Initializing Parallel LINear Constraint Solver
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess
P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 116-122
-------- -------- — Thank You — -------- --------
The number of constraints is 2333
There are constraints between atoms in different decomposition domains,
will communicate selected coordinates each lincs iteration
++++ 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 — -------- --------
Intra-simulation communication will occur every 10 steps.
++++ 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 — -------- --------
There are: 51659 Atoms
Atom distribution over 49 domains: av 1054 stddev 35 min 996 max 1122
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest
Started mdrun on rank 0 Thu May 9 00:08:48 2024
Step Time
0 0.00000
Energies (kJ/mol)
Bond U-B Proper Dih. Improper Dih. CMAP Dih.
3.85695e+03 1.08233e+04 1.24223e+04 6.64243e+02 -3.68648e+02
LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.
4.02752e+03 5.04419e+04 6.03038e+04 -8.10621e+05 2.51307e+03
Potential Kinetic En. Total Energy Conserved En. Temperature
-6.65937e+05 1.31726e+05 -5.34210e+05 -5.34180e+05 2.99833e+02
Pressure (bar) Constr. rmsd
2.85752e+01 3.33859e-06
DD step 79 load imb.: force 11.6% pme mesh/force 0.492
step 240 Turning on dynamic load balancing, because the performance loss due to load imbalance is 5.6 %.
Step Time
5000 10.00000
Energies (kJ/mol)
Bond U-B Proper Dih. Improper Dih. CMAP Dih.
3.95122e+03 1.09889e+04 1.23460e+04 6.18268e+02 -4.50679e+02
LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.
3.80860e+03 5.02288e+04 6.07906e+04 -8.10765e+05 2.42138e+03
Potential Kinetic En. Total Energy Conserved En. Temperature
-6.66062e+05 1.32096e+05 -5.33966e+05 -5.34083e+05 3.00674e+02
Pressure (bar) Constr. rmsd
-4.51211e+01 3.29013e-06
DD step 9999 vol min/aver 0.877 load imb.: force 4.5% pme mesh/force 0.490
Step Time
10000 20.00000
Energies (kJ/mol)
Bond U-B Proper Dih. Improper Dih. CMAP Dih.
3.97649e+03 1.06274e+04 1.23479e+04 6.00813e+02 -4.52109e+02
LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.
4.06390e+03 5.04673e+04 5.95876e+04 -8.09761e+05 2.44050e+03
Potential Kinetic En. Total Energy Conserved En. Temperature
-6.66101e+05 1.31085e+05 -5.35016e+05 -5.33972e+05 2.98373e+02
Pressure (bar) Constr. rmsd
-1.63797e+01 2.95202e-06
step 14400 Turning off dynamic load balancing, because it is degrading performance.
Atom distribution over 49 domains: av 1054 stddev 31 min 1014 max 1104
Step Time
15000 30.00000
Energies (kJ/mol)
Bond U-B Proper Dih. Improper Dih. CMAP Dih.
3.76916e+03 1.09247e+04 1.22990e+04 6.46692e+02 -4.39659e+02
LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.
3.93045e+03 5.02139e+04 6.26199e+04 -8.14065e+05 2.44340e+03
Potential Kinetic En. Total Energy Conserved En. Temperature
-6.67657e+05 1.31792e+05 -5.35865e+05 -5.33885e+05 2.99984e+02
Pressure (bar) Constr. rmsd
2.80120e+02 3.16420e-06