A series of Python3 script to lower the barrier of computing and simulating molecular and material systems.
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:-) GROMACS - gmx mdrun, 2020.6-Debian-2020.6-2 (-:
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 Artem Zhmurov
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) 2001-2019, 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 2020.6-Debian-2020.6-2
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /home/student/adit/CMMDE_launching/larutan/SistemLarutan
Process ID: 2570737
Command line:
gmx -quiet mdrun -deffnm nvt -ntmpi 1 -v true
GROMACS version: 2020.6-Debian-2020.6-2
Precision: single
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support: disabled
SIMD instructions: SSE4.1
FFT library: fftw-3.3.8-sse2-avx
RDTSCP usage: disabled
TNG support: enabled
Hwloc support: hwloc-2.4.1
Tracing support: disabled
C compiler: /usr/bin/cc GNU 10.2.1
C compiler flags: -msse4.1 -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG
C++ compiler: /usr/bin/c++ GNU 10.2.1
C++ compiler flags: -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG
Running on 1 node with total 1 cores, 2 logical cores
Hardware detected:
CPU info:
Vendor: Intel
Brand: Intel(R) Xeon(R) CPU @ 2.20GHz
Family: 6 Model: 79 Stepping: 0
Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 x2apic
Hardware topology: Full, with devices
Sockets, cores, and logical processors:
Socket 0: [ 0 1]
Numa nodes:
Node 0 (8343068672 bytes mem): 0 1
Latency:
0
0 1.00
Caches:
L1: 32768 bytes, linesize 64 bytes, assoc. 8, shared 2 ways
L2: 262144 bytes, linesize 64 bytes, assoc. 8, shared 2 ways
L3: 57671680 bytes, linesize 64 bytes, assoc. 20, shared 2 ways
PCI devices:
0000:00:04.0 Id: 1af4:1000 Class: 0x0200 Numa: 0
Highest SIMD level requested by all nodes in run: AVX2_256
SIMD instructions selected at compile time: SSE4.1
This program was compiled for different hardware than you are running on,
which could influence performance.
The current CPU can measure timings more accurately than the code in
gmx mdrun was configured to use. This might affect your simulation
speed as accurate timings are needed for load-balancing.
Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
++++ 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 --- -------- --------
The number of OpenMP threads was set by environment variable OMP_NUM_THREADS to 1
Input Parameters:
integrator = md
tinit = 0
dt = 0.001
nsteps = 1000
init-step = 0
simulation-part = 1
comm-mode = Linear
nstcomm = 100
bd-fric = 0
ld-seed = 2101298815
emtol = 10
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
rtpi = 0.05
nstxout = 100
nstvout = 0
nstfout = 0
nstlog = 1000
nstcalcenergy = 100
nstenergy = 1000
nstxout-compressed = 0
compressed-x-precision = 1000
cutoff-scheme = Verlet
nstlist = 10
pbc = xyz
periodic-molecules = false
verlet-buffer-tolerance = 0.005
rlist = 0.961399
coulombtype = PME
coulomb-modifier = Potential-shift
rcoulomb-switch = 0
rcoulomb = 0.961399
epsilon-r = 1
epsilon-rf = inf
vdw-type = Cut-off
vdw-modifier = Potential-shift
rvdw-switch = 0
rvdw = 0.961399
DispCorr = EnerPres
table-extension = 1
fourierspacing = 0.16
fourier-nx = 14
fourier-ny = 14
fourier-nz = 14
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 = 10
nh-chain-length = 0
print-nose-hoover-chain-variables = false
pcoupl = No
pcoupltype = Isotropic
nstpcouple = -1
tau-p = 1
compressibility (3x3):
compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref-p (3x3):
ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+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
QMconstraints = 0
QMMMscheme = 0
MMChargeScaleFactor = 1
qm-opts:
ngQM = 0
constraint-algorithm = Lincs
continuation = false
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
grpopts:
nrdf: 1012
ref-t: 298.15
tau-t: 0.1
annealing: No
annealing-npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp-flags[ 0]: 0
Changing nstlist from 10 to 100, rlist from 0.961399 to 0.961399
Using 1 MPI thread
Non-default thread affinity set, disabling internal thread affinity
Using 1 OpenMP thread
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 0.307804 nm for Ewald
Potential shift: LJ r^-12: -1.604e+00 r^-6: -1.266e+00, Ewald -1.040e-05
Initialized non-bonded Ewald tables, spacing: 9.15e-04 size: 1052
Generated table with 980 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 980 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 980 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Using SIMD 4x4 nonbonded short-range kernels
Using a 4x4 pair-list setup:
updated every 100 steps, buffer 0.000 nm, rlist 0.961 nm
At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
updated every 100 steps, buffer 0.119 nm, rlist 1.080 nm
Using Lorentz-Berthelot Lennard-Jones combination rule
Long Range LJ corr.: <C6> 3.6868e-04
Removing pbc first time
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 281
++++ 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: 432 Atoms
Constraining the starting coordinates (step 0)
Constraining the coordinates at t0-dt (step 0)
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest
RMS relative constraint deviation after constraining: 6.46e-07
Initial temperature: 303.569 K
Started mdrun on rank 0 Tue Jun 7 16:54:18 2022
Step Time
0 0.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
7.53202e+00 3.22554e+01 2.42243e+01 2.97818e+01 -4.76251e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-2.50927e+03 -4.22464e+02 -3.37410e+01 -1.66597e+01 3.19699e+01
Potential Kinetic En. Total Energy Conserved En. Temperature
-2.86113e+03 1.27811e+03 -1.58303e+03 -1.58303e+03 3.03797e+02
Pres. DC (bar) Pressure (bar) Constr. rmsd
-5.87450e+01 -3.42106e+01 6.57980e-07
Step Time
1000 1.00000
Writing checkpoint, step 1000 at Tue Jun 7 16:54:18 2022
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
3.51747e+01 1.84321e+02 3.77233e+01 7.31505e+01 -4.79605e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-2.52513e+03 -3.16425e+02 -3.37410e+01 2.95999e+02 7.23590e+01
Potential Kinetic En. Total Energy Conserved En. Temperature
-2.18136e+03 1.20932e+03 -9.72044e+02 -1.57863e+03 2.87446e+02
Pres. DC (bar) Pressure (bar) Constr. rmsd
-5.87450e+01 5.07352e+02 7.49168e-07
<====== ############### ==>
<==== A V E R A G E S ====>
<== ############### ======>
Statistics over 1001 steps using 11 frames
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
2.26678e+01 1.50638e+02 3.84769e+01 5.46640e+01 -4.77874e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-2.52157e+03 -3.37459e+02 -3.37410e+01 2.26510e+02 6.15578e+01
Potential Kinetic En. Total Energy Conserved En. Temperature
-2.34303e+03 1.25062e+03 -1.09241e+03 -1.57934e+03 2.97264e+02
Pres. DC (bar) Pressure (bar) Constr. rmsd
-5.87450e+01 4.33180e+02 0.00000e+00
Total Virial (kJ/mol)
2.27897e+02 -2.39683e+01 -4.34334e+01
-2.39683e+01 3.04155e+02 3.35767e+01
-4.34333e+01 3.35766e+01 3.44256e+02
Pressure (bar)
6.59207e+02 1.12818e+02 1.55373e+02
1.12819e+02 3.63445e+02 -1.56211e+02
1.55372e+02 -1.56210e+02 2.76890e+02
M E G A - F L O P S A C C O U N T I N G
NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels
RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table
W3=SPC/TIP3p W4=TIP4p (single or pairs)
V&F=Potential and force V=Potential only F=Force only
Computing: M-Number M-Flops % Flops
-----------------------------------------------------------------------------
Pair Search distance check 0.748886 6.740 0.2
NxN QSTab Elec. + LJ [F] 52.605432 2156.823 53.2
NxN QSTab Elec. + LJ [V&F] 0.585672 34.555 0.9
NxN QSTab Elec. [F] 28.093032 955.163 23.6
NxN QSTab Elec. [V&F] 0.312632 12.818 0.3
1,4 nonbonded interactions 0.072072 6.486 0.2
Calc Weights 1.297296 46.703 1.2
Spread Q Bspline 27.675648 55.351 1.4
Gather F Bspline 27.675648 166.054 4.1
3D-FFT 62.746684 501.973 12.4
Solve PME 0.196196 12.557 0.3
Shift-X 0.004752 0.029 0.0
Bonds 0.027027 1.595 0.0
Angles 0.226226 38.006 0.9
Propers 0.027027 6.189 0.2
RB-Dihedrals 0.072072 17.802 0.4
Virial 0.005247 0.094 0.0
Stop-CM 0.005184 0.052 0.0
Calc-Ekin 0.087264 2.356 0.1
Lincs 0.281843 16.911 0.4
Lincs-Mat 1.961868 7.847 0.2
Constraint-V 0.563124 4.505 0.1
Constraint-Vir 0.003091 0.074 0.0
-----------------------------------------------------------------------------
Total 4050.682 100.0
-----------------------------------------------------------------------------
R E A L C Y C L E A N D T I M E A C C O U N T I N G
On 1 MPI rank
Computing: Num Num Call Wall time Giga-Cycles
Ranks Threads Count (s) total sum %
-----------------------------------------------------------------------------
Neighbor search 1 1 11 0.009 0.019 1.4
Force 1 1 1001 0.400 0.881 65.8
PME mesh 1 1 1001 0.136 0.299 22.4
NB X/F buffer ops. 1 1 1991 0.005 0.011 0.8
Write traj. 1 1 11 0.025 0.056 4.2
Update 1 1 1001 0.004 0.009 0.7
Constraints 1 1 1003 0.023 0.050 3.7
Rest 0.006 0.013 1.0
-----------------------------------------------------------------------------
Total 0.609 1.339 100.0
-----------------------------------------------------------------------------
Breakdown of PME mesh computation
-----------------------------------------------------------------------------
PME spread 1 1 1001 0.040 0.088 6.6
PME gather 1 1 1001 0.055 0.122 9.1
PME 3D-FFT 1 1 2002 0.024 0.053 3.9
PME solve Elec 1 1 1001 0.016 0.035 2.6
-----------------------------------------------------------------------------
Core t (s) Wall t (s) (%)
Time: 0.608 0.609 100.0
(ns/day) (hour/ns)
Performance: 142.115 0.169
Finished mdrun on rank 0 Tue Jun 7 16:54:18 2022