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A series of Python3 script to lower the barrier of computing and simulating molecular and material systems.
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CMMDE/examples/larutan/UreaAirAmonia/SistemLarutan/nvep.log

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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: 2570744
Command line:
gmx -quiet mdrun -deffnm nvep -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 = 0.0005
nsteps = 10000
init-step = 0
simulation-part = 1
comm-mode = Linear
nstcomm = 100
bd-fric = 0
ld-seed = -140560403
emtol = 10
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
rtpi = 0.05
nstxout = 500
nstvout = 500
nstfout = 0
nstlog = 500
nstcalcenergy = 100
nstenergy = 500
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 = No
nsttcouple = -1
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 = 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
grpopts:
nrdf: 1293
ref-t: 0
tau-t: 0
annealing: No
annealing-npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp-flags[ 0]: 0
Can not increase nstlist because an NVE ensemble is used
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 10 steps, buffer 0.000 nm, rlist 0.961 nm
Using Lorentz-Berthelot Lennard-Jones combination rule
Long Range LJ corr.: <C6> 3.6868e-04
There are: 432 Atoms
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 Tue Jun 7 16:54:20 2022
Step Time
0 0.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
2.68571e+01 2.06130e+02 3.50263e+01 4.98516e+01 -4.70008e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-2.50551e+03 -3.10729e+02 -3.31483e+01 3.11356e+02 6.78661e+01
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-2.15700e+03 1.17316e+03 -9.83849e+02 2.18249e+02 -5.67052e+01
Pressure (bar)
7.97352e+02
Step Time
500 0.25000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
5.71829e+01 1.80092e+02 3.09587e+01 5.62519e+01 -4.70784e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-2.50986e+03 -2.95917e+02 -3.31483e+01 2.92289e+02 7.71216e+01
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-2.14974e+03 1.16607e+03 -9.83664e+02 2.16932e+02 -5.67052e+01
Pressure (bar)
2.98072e+02
Step Time
1000 0.50000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
6.69650e+01 2.01878e+02 3.47275e+01 5.17517e+01 -4.74050e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-2.51733e+03 -3.14749e+02 -3.31483e+01 2.74665e+02 7.15622e+01
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-2.16842e+03 1.18507e+03 -9.83349e+02 2.20466e+02 -5.67052e+01
Pressure (bar)
4.11046e+01
Step Time
1500 0.75000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
5.89589e+01 2.01801e+02 2.84650e+01 4.74906e+01 -4.65939e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-2.50063e+03 -3.40624e+02 -3.31483e+01 2.76941e+02 8.30847e+01
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-2.18232e+03 1.19856e+03 -9.83759e+02 2.22976e+02 -5.67052e+01
Pressure (bar)
5.79724e+02
Step Time
2000 1.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
8.35276e+01 1.92469e+02 3.61053e+01 5.95481e+01 -4.75944e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-2.53029e+03 -3.26461e+02 -3.31483e+01 2.72068e+02 7.07096e+01
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-2.18023e+03 1.19672e+03 -9.83508e+02 2.22634e+02 -5.67052e+01
Pressure (bar)
4.29622e+02
Step Time
2500 1.25000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
7.04942e+01 1.88806e+02 4.12116e+01 6.39807e+01 -4.84451e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-2.53973e+03 -2.89260e+02 -3.31483e+01 2.52880e+02 6.06684e+01
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-2.18894e+03 1.20491e+03 -9.84036e+02 2.24156e+02 -5.67052e+01
Pressure (bar)
7.94977e+02
Step Time
3000 1.50000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
6.47645e+01 1.71579e+02 2.34261e+01 5.25431e+01 -4.67042e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-2.50095e+03 -3.07265e+02 -3.31483e+01 2.95478e+02 7.64883e+01
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-2.16176e+03 1.17794e+03 -9.83812e+02 2.19140e+02 -5.67052e+01
Pressure (bar)
5.99587e+02
Step Time
3500 1.75000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
9.43893e+01 1.61463e+02 2.44596e+01 6.38215e+01 -4.68754e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-2.50223e+03 -2.84392e+02 -3.31483e+01 2.26656e+02 6.90088e+01
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-2.18466e+03 1.20142e+03 -9.83235e+02 2.23508e+02 -5.67052e+01
Pressure (bar)
3.79233e+02
Step Time
4000 2.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
9.04692e+01 1.52852e+02 2.61851e+01 4.55728e+01 -4.76396e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-2.52034e+03 -3.01335e+02 -3.31483e+01 2.98707e+02 7.06226e+01
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-2.17518e+03 1.19173e+03 -9.83449e+02 2.21705e+02 -5.67052e+01
Pressure (bar)
9.28437e+02
Step Time
4500 2.25000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
8.07335e+01 1.79767e+02 4.54518e+01 5.96417e+01 -4.80120e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-2.52796e+03 -3.17002e+02 -3.31483e+01 3.03310e+02 7.60940e+01
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-2.13792e+03 1.15426e+03 -9.83658e+02 2.14734e+02 -5.67052e+01
Pressure (bar)
-3.71822e+02
Step Time
5000 2.50000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
8.83895e+01 1.35048e+02 4.58026e+01 7.27292e+01 -4.87079e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-2.52845e+03 -3.30437e+02 -3.31483e+01 2.83694e+02 7.64058e+01
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-2.19483e+03 1.21136e+03 -9.83477e+02 2.25356e+02 -5.67052e+01
Pressure (bar)
-4.40553e+02
Step Time
5500 2.75000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
8.33474e+01 1.60111e+02 2.49346e+01 4.50281e+01 -4.84969e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-2.52294e+03 -3.44011e+02 -3.31483e+01 2.92817e+02 7.44514e+01
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-2.22426e+03 1.24060e+03 -9.83656e+02 2.30797e+02 -5.67052e+01
Pressure (bar)
1.18631e+03
Step Time
6000 3.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
6.61491e+01 1.99206e+02 2.83812e+01 4.32869e+01 -4.63137e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-2.50879e+03 -3.48650e+02 -3.31483e+01 3.06267e+02 7.48799e+01
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-2.17705e+03 1.19348e+03 -9.83563e+02 2.22031e+02 -5.67052e+01
Pressure (bar)
-3.32347e+02
Step Time
6500 3.25000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
8.83938e+01 1.59127e+02 4.40262e+01 6.20234e+01 -4.86572e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-2.52597e+03 -3.25515e+02 -3.31483e+01 2.94908e+02 7.41591e+01
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-2.16686e+03 1.18353e+03 -9.83332e+02 2.20180e+02 -5.67052e+01
Pressure (bar)
4.52560e+02
Step Time
7000 3.50000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
8.94784e+01 1.77594e+02 2.43321e+01 3.49407e+01 -4.80416e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-2.52508e+03 -3.12532e+02 -3.31483e+01 2.73032e+02 6.57994e+01
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-2.21039e+03 1.22704e+03 -9.83349e+02 2.28273e+02 -5.67052e+01
Pressure (bar)
8.73185e+02
Step Time
7500 3.75000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
9.28125e+01 1.62232e+02 3.35552e+01 5.94787e+01 -4.71466e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-2.51767e+03 -2.95079e+02 -3.31483e+01 2.72958e+02 7.00983e+01
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-2.15948e+03 1.17609e+03 -9.83393e+02 2.18795e+02 -5.67052e+01
Pressure (bar)
-5.48705e+02
Step Time
8000 4.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
9.96638e+01 1.62056e+02 2.80954e+01 5.80195e+01 -4.63848e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-2.49588e+03 -3.25313e+02 -3.31483e+01 2.86824e+02 7.14535e+01
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-2.15287e+03 1.16952e+03 -9.83342e+02 2.17574e+02 -5.67052e+01
Pressure (bar)
2.97416e+02
Step Time
8500 4.25000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
9.72742e+01 1.36549e+02 4.99397e+01 7.40676e+01 -4.85137e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-2.54643e+03 -2.83260e+02 -3.31483e+01 3.23393e+02 6.66151e+01
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-2.11986e+03 1.13679e+03 -9.83069e+02 2.11484e+02 -5.67052e+01
Pressure (bar)
9.45151e+02
Step Time
9000 4.50000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
8.24089e+01 1.79101e+02 3.29559e+01 4.82325e+01 -4.74104e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-2.51091e+03 -2.87232e+02 -3.31483e+01 2.83039e+02 6.98197e+01
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-2.14047e+03 1.15701e+03 -9.83462e+02 2.15245e+02 -5.67052e+01
Pressure (bar)
5.52506e+02
Step Time
9500 4.75000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
8.46766e+01 1.58841e+02 4.20994e+01 6.14774e+01 -4.84161e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-2.52382e+03 -2.96920e+02 -3.31483e+01 2.45470e+02 6.73681e+01
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-2.19880e+03 1.21528e+03 -9.83517e+02 2.26086e+02 -5.67052e+01
Pressure (bar)
-5.11383e+02
Step Time
10000 5.00000
Writing checkpoint, step 10000 at Tue Jun 7 16:54:27 2022
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
8.67398e+01 1.65914e+02 5.29682e+01 6.75271e+01 -4.83456e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-2.53760e+03 -3.09650e+02 -3.31483e+01 3.06939e+02 6.95346e+01
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-2.13561e+03 1.15236e+03 -9.83256e+02 2.14380e+02 -5.67052e+01
Pressure (bar)
4.15713e+02
<====== ############### ==>
<==== A V E R A G E S ====>
<== ############### ======>
Statistics over 10001 steps using 101 frames
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
8.47749e+01 1.65731e+02 3.59536e+01 5.62230e+01 -4.76393e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-2.51942e+03 -3.09137e+02 -3.31483e+01 2.87991e+02 7.15408e+01
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-2.16426e+03 1.18071e+03 -9.83545e+02 2.19655e+02 -5.67052e+01
Pressure (bar)
3.09581e+02
Total Virial (kJ/mol)
2.92701e+02 2.08917e+01 -3.05352e+00
2.08916e+01 3.00999e+02 4.96721e-02
-3.05346e+00 4.97567e-02 3.14731e+02
Pressure (bar)
3.54393e+02 -9.94881e+01 1.26737e+01
-9.94881e+01 3.11738e+02 -1.17409e+01
1.26735e+01 -1.17412e+01 2.62611e+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 69.718542 627.467 1.5
NxN QSTab Elec. + LJ [F] 519.912272 21316.403 52.3
NxN QSTab Elec. + LJ [V&F] 5.310760 313.335 0.8
NxN QSTab Elec. [F] 283.296912 9632.095 23.7
NxN QSTab Elec. [V&F] 2.910824 119.344 0.3
1,4 nonbonded interactions 0.720072 64.806 0.2
Calc Weights 12.961296 466.607 1.1
Spread Q Bspline 276.507648 553.015 1.4
Gather F Bspline 276.507648 1659.046 4.1
3D-FFT 626.902684 5015.221 12.3
Solve PME 1.960196 125.453 0.3
Shift-X 0.432432 2.595 0.0
Bonds 3.080308 181.738 0.4
Angles 2.260226 379.718 0.9
Propers 0.270027 61.836 0.2
RB-Dihedrals 0.720072 177.858 0.4
Virial 0.048177 0.867 0.0
Stop-CM 0.043632 0.436 0.0
Calc-Ekin 0.864864 23.351 0.1
-----------------------------------------------------------------------------
Total 40721.192 100.0
-----------------------------------------------------------------------------
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 1001 0.836 1.840 11.0
Force 1 1 10001 4.878 10.732 64.4
PME mesh 1 1 10001 1.647 3.623 21.7
NB X/F buffer ops. 1 1 19001 0.061 0.133 0.8
Write traj. 1 1 21 0.022 0.048 0.3
Update 1 1 10001 0.045 0.099 0.6
Rest 0.089 0.195 1.2
-----------------------------------------------------------------------------
Total 7.577 16.670 100.0
-----------------------------------------------------------------------------
Breakdown of PME mesh computation
-----------------------------------------------------------------------------
PME spread 1 1 10001 0.469 1.031 6.2
PME gather 1 1 10001 0.676 1.486 8.9
PME 3D-FFT 1 1 20002 0.296 0.651 3.9
PME solve Elec 1 1 10001 0.194 0.428 2.6
-----------------------------------------------------------------------------
NOTE: 11 % of the run time was spent in pair search,
you might want to increase nstlist (this has no effect on accuracy)
Core t (s) Wall t (s) (%)
Time: 7.577 7.577 100.0
(ns/day) (hour/ns)
Performance: 57.020 0.421
Finished mdrun on rank 0 Tue Jun 7 16:54:27 2022