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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/UreaAir/SistemLarutan/nvep.log

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:-) GROMACS - gmx mdrun, 2021.3 (-:
GROMACS is written by:
Andrey Alekseenko 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
Gilles Gouaillardet 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 2021.3
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /home/adit/MySoftware/CMMDE/test/larutan/SistemLarutan
Process ID: 58606
Command line:
gmx -quiet mdrun -deffnm nvep -ntmpi 1 -v true
GROMACS version: 2021.3
Verified release checksum is c5bf577cc74de0e05106b7b6426476abb7f6530be7b4a2c64f637d6a6eca8fcb
Precision: mixed
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support: disabled
SIMD instructions: AVX2_256
FFT library: fftw-3.3.8-sse2-avx-avx2-avx2_128
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: disabled
Tracing support: disabled
C compiler: /usr/bin/cc GNU 9.3.0
C compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG
C++ compiler: /usr/bin/c++ GNU 9.3.0
C++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG
Running on 1 node with total 4 cores, 8 logical cores
Hardware detected:
CPU info:
Vendor: Intel
Brand: 11th Gen Intel(R) Core(TM) i7-1165G7 @ 2.80GHz
Family: 6 Model: 140 Stepping: 1
Features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl avx512secondFMA clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
Number of AVX-512 FMA units: 1 (AVX2 is faster w/o 2 AVX-512 FMA units)
Hardware topology: Basic
Sockets, cores, and logical processors:
Socket 0: [ 0 4] [ 1 5] [ 2 6] [ 3 7]
++++ 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.5053201
-------- -------- --- 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
mts = false
comm-mode = Linear
nstcomm = 100
bd-fric = 0
ld-seed = -1646010373
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 = 0.711399
coulombtype = PME
coulomb-modifier = Potential-shift
rcoulomb-switch = 0
rcoulomb = 0.711399
epsilon-r = 1
epsilon-rf = inf
vdw-type = Cut-off
vdw-modifier = Potential-shift
rvdw-switch = 0
rvdw = 0.711399
DispCorr = EnerPres
table-extension = 1
fourierspacing = 0.16
fourier-nx = 12
fourier-ny = 12
fourier-nz = 12
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
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 =
grpopts:
nrdf: 1209
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
Using 1 OpenMP thread
NOTE: Thread affinity was not set.
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 0.227763 nm for Ewald
Potential shift: LJ r^-12: -5.952e+01 r^-6: -7.715e+00, Ewald -1.406e-05
Initialized non-bonded Ewald tables, spacing: 7.87e-04 size: 905
Generated table with 855 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 855 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 855 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Long Range LJ corr.: <C6> 4.1484e-04
Using SIMD 4x8 nonbonded short-range kernels
Using a 4x8 pair-list setup:
updated every 10 steps, buffer 0.000 nm, rlist 0.711 nm
Using Lorentz-Berthelot Lennard-Jones combination rule
There are: 404 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 Thu Apr 28 23:06:12 2022
Step Time
0 0.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
5.99428e+01 3.56180e+02 1.08426e+02 6.24313e+01 -6.83991e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-3.66811e+03 -1.26387e+02 -1.88869e+02 -2.39119e+03 1.31181e+02
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-5.66323e+03 1.12513e+03 -4.53810e+03 2.23858e+02 -7.58989e+02
Pressure (bar)
9.98538e+03
Step Time
500 0.25000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
3.25881e+02 2.33194e+02 7.37560e+01 5.42421e+01 -6.90217e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-3.67396e+03 -2.67822e+01 -1.88869e+02 -2.74424e+03 1.45849e+02
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-5.80783e+03 1.26905e+03 -4.53878e+03 2.52492e+02 -7.58989e+02
Pressure (bar)
-8.07414e+03
Step Time
1000 0.50000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
2.54823e+02 2.79331e+02 6.62055e+01 4.20885e+01 -6.77376e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-3.64784e+03 1.66437e+01 -1.88869e+02 -2.69774e+03 1.18650e+02
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-5.76348e+03 1.22477e+03 -4.53871e+03 2.43683e+02 -7.58989e+02
Pressure (bar)
1.19652e+03
Step Time
1500 0.75000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
2.34694e+02 2.58759e+02 1.00357e+02 6.36489e+01 -6.95575e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-3.67504e+03 -8.12779e+01 -1.88869e+02 -2.59040e+03 1.27310e+02
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-5.75777e+03 1.21899e+03 -4.53878e+03 2.42532e+02 -7.58989e+02
Pressure (bar)
7.92818e+02
Step Time
2000 1.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
2.96694e+02 3.11317e+02 7.99523e+01 6.08277e+01 -6.78185e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-3.66116e+03 -5.44866e+01 -1.88869e+02 -2.70159e+03 1.22550e+02
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-5.74154e+03 1.20322e+03 -4.53832e+03 2.39395e+02 -7.58989e+02
Pressure (bar)
-4.60449e+03
Step Time
2500 1.25000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
2.52754e+02 2.93479e+02 8.33528e+01 6.02577e+01 -6.93942e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-3.67242e+03 -4.20954e+01 -1.88869e+02 -2.68881e+03 1.27354e+02
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-5.78193e+03 1.24283e+03 -4.53910e+03 2.47276e+02 -7.58989e+02
Pressure (bar)
5.62425e+02
Step Time
3000 1.50000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
2.97143e+02 2.69501e+02 8.74233e+01 6.83455e+01 -7.12990e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-3.69489e+03 7.64003e+01 -1.88869e+02 -2.84679e+03 1.25492e+02
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-5.81337e+03 1.27466e+03 -4.53871e+03 2.53608e+02 -7.58989e+02
Pressure (bar)
9.92100e+02
Step Time
3500 1.75000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
2.89762e+02 2.85771e+02 8.38730e+01 5.10484e+01 -6.79658e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-3.65433e+03 2.62536e+01 -1.88869e+02 -2.77233e+03 1.29480e+02
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-5.75614e+03 1.21805e+03 -4.53809e+03 2.42345e+02 -7.58989e+02
Pressure (bar)
2.45534e+02
Step Time
4000 2.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
2.54975e+02 3.18450e+02 7.77050e+01 5.47855e+01 -6.72105e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-3.64533e+03 -9.41769e+01 -1.88869e+02 -2.61913e+03 1.42950e+02
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-5.70537e+03 1.16719e+03 -4.53818e+03 2.32225e+02 -7.58989e+02
Pressure (bar)
-3.35894e+03
Step Time
4500 2.25000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
3.33481e+02 3.04330e+02 6.62906e+01 4.86214e+01 -7.00843e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-3.68251e+03 2.42634e+00 -1.88869e+02 -2.80236e+03 1.24136e+02
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-5.80146e+03 1.26328e+03 -4.53819e+03 2.51343e+02 -7.58989e+02
Pressure (bar)
2.14624e+02
Step Time
5000 2.50000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
3.39930e+02 2.92891e+02 6.96768e+01 4.67481e+01 -6.73381e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-3.64604e+03 1.34066e+01 -1.88869e+02 -2.77588e+03 1.32168e+02
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-5.72271e+03 1.18527e+03 -4.53744e+03 2.35823e+02 -7.58989e+02
Pressure (bar)
-4.56350e+03
Step Time
5500 2.75000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
2.52495e+02 2.35887e+02 8.33571e+01 5.38983e+01 -6.82821e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-3.67800e+03 -4.82545e+01 -1.88869e+02 -2.61424e+03 1.47474e+02
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-5.76308e+03 1.22459e+03 -4.53849e+03 2.43646e+02 -7.58989e+02
Pressure (bar)
-1.02638e+03
Step Time
6000 3.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
3.13147e+02 2.39011e+02 7.33941e+01 5.34968e+01 -6.90967e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-3.66805e+03 -2.18502e+01 -1.88869e+02 -2.66729e+03 1.24804e+02
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-5.74912e+03 1.21058e+03 -4.53853e+03 2.40860e+02 -7.58989e+02
Pressure (bar)
1.27520e+02
Step Time
6500 3.25000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
3.09016e+02 2.67246e+02 7.87046e+01 4.63376e+01 -6.84008e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-3.65858e+03 -2.66303e+01 -1.88869e+02 -2.75379e+03 1.41538e+02
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-5.79187e+03 1.25337e+03 -4.53850e+03 2.49372e+02 -7.58989e+02
Pressure (bar)
-7.49130e+02
Step Time
7000 3.50000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
3.09334e+02 2.45946e+02 7.02546e+01 4.56670e+01 -6.84456e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-3.65914e+03 2.07605e+01 -1.88869e+02 -2.71921e+03 1.12711e+02
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-5.76939e+03 1.23114e+03 -4.53825e+03 2.44950e+02 -7.58989e+02
Pressure (bar)
1.46120e+03
Step Time
7500 3.75000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
3.49179e+02 2.52384e+02 9.55043e+01 7.34459e+01 -6.93976e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-3.68927e+03 -1.31437e+01 -1.88869e+02 -2.71160e+03 1.24890e+02
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-5.71442e+03 1.17642e+03 -4.53800e+03 2.34063e+02 -7.58989e+02
Pressure (bar)
-1.39160e+03
Step Time
8000 4.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
3.01540e+02 2.89778e+02 7.96111e+01 5.42763e+01 -6.87444e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-3.67127e+03 2.74904e+01 -1.88869e+02 -2.70070e+03 1.34246e+02
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-5.68078e+03 1.14344e+03 -4.53733e+03 2.27501e+02 -7.58989e+02
Pressure (bar)
1.73129e+03
Step Time
8500 4.25000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
2.89698e+02 2.90379e+02 7.49347e+01 5.73303e+01 -6.88700e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-3.66852e+03 -7.42266e+01 -1.88869e+02 -2.63272e+03 1.30490e+02
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-5.72838e+03 1.19016e+03 -4.53823e+03 2.36795e+02 -7.58989e+02
Pressure (bar)
6.72412e+02
Step Time
9000 4.50000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
3.07260e+02 2.93818e+02 7.52461e+01 4.52379e+01 -6.95643e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-3.68113e+03 -1.77533e+01 -1.88869e+02 -2.69938e+03 1.30683e+02
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-5.74184e+03 1.20329e+03 -4.53855e+03 2.39408e+02 -7.58989e+02
Pressure (bar)
-9.66020e+02
Step Time
9500 4.75000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
3.28822e+02 2.95144e+02 9.61802e+01 6.31835e+01 -6.87580e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-3.66657e+03 6.08919e+00 -1.88869e+02 -2.85020e+03 1.23600e+02
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-5.79949e+03 1.26174e+03 -4.53775e+03 2.51039e+02 -7.58989e+02
Pressure (bar)
1.07906e+03
Step Time
10000 5.00000
Writing checkpoint, step 10000 at Thu Apr 28 23:06:14 2022
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
3.43095e+02 3.02972e+02 8.56095e+01 5.28222e+01 -6.79941e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-3.64613e+03 4.37440e+01 -1.88869e+02 -2.85200e+03 1.21920e+02
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-5.74364e+03 1.20669e+03 -4.53695e+03 2.40084e+02 -7.58989e+02
Pressure (bar)
-2.16015e+03
Energy conservation over simulation part #1 of length 5 ns, time 0 to 5 ns
Conserved energy drift: 5.67e-04 kJ/mol/ps per atom
<====== ############### ==>
<==== A V E R A G E S ====>
<== ############### ======>
Statistics over 10001 steps using 101 frames
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
2.92533e+02 2.81408e+02 8.22884e+01 5.44070e+01 -6.86595e+00
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-3.66662e+03 -1.00313e+01 -1.88869e+02 -2.72729e+03 1.31145e+02
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-5.75789e+03 1.21962e+03 -4.53827e+03 2.42658e+02 -7.58989e+02
Pressure (bar)
-7.07579e+02
Total Virial (kJ/mol)
4.81421e+02 -5.11129e+00 -4.31531e+00
-5.11134e+00 5.01042e+02 2.15936e+01
-4.31542e+00 2.15934e+01 5.02170e+02
Pressure (bar)
-6.17553e+02 1.73841e+01 4.89267e+01
1.73845e+01 -7.36802e+02 -1.94815e+02
4.89275e+01 -1.94814e+02 -7.68383e+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 86.774298 780.969 1.2
NxN Ewald Elec. + LJ [F] 554.883184 36622.290 57.1
NxN Ewald Elec. + LJ [V&F] 5.670848 606.781 0.9
NxN Ewald Elec. [F] 316.401424 19300.487 30.1
NxN Ewald Elec. [V&F] 3.224800 270.883 0.4
1,4 nonbonded interactions 1.040104 93.609 0.1
Calc Weights 12.121212 436.364 0.7
Spread Q Bspline 258.585856 517.172 0.8
Gather F Bspline 258.585856 1551.515 2.4
3D-FFT 371.717168 2973.737 4.6
Solve PME 1.440144 92.169 0.1
Shift-X 0.404404 2.426 0.0
Bonds 2.910291 171.707 0.3
Angles 2.170217 364.596 0.6
Propers 1.040104 238.184 0.4
Impropers 0.390039 81.128 0.1
Virial 0.045349 0.816 0.0
Stop-CM 0.040804 0.408 0.0
Calc-Ekin 0.808808 21.838 0.0
-----------------------------------------------------------------------------
Total 64127.080 100.0
-----------------------------------------------------------------------------
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 0.355 0.996 17.4
Force 1 1 10001 1.211 3.396 59.2
PME mesh 1 1 10001 0.411 1.151 20.1
NB X/F buffer ops. 1 1 19001 0.017 0.049 0.9
Write traj. 1 1 21 0.023 0.064 1.1
Update 1 1 10001 0.012 0.033 0.6
Rest 0.016 0.044 0.8
-----------------------------------------------------------------------------
Total 2.045 5.733 100.0
-----------------------------------------------------------------------------
Breakdown of PME mesh computation
-----------------------------------------------------------------------------
PME spread 1 1 10001 0.176 0.492 8.6
PME gather 1 1 10001 0.129 0.363 6.3
PME 3D-FFT 1 1 20002 0.051 0.143 2.5
PME solve Elec 1 1 10001 0.052 0.145 2.5
-----------------------------------------------------------------------------
NOTE: 17 % 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: 2.045 2.045 100.0
(ns/day) (hour/ns)
Performance: 211.244 0.114
Finished mdrun on rank 0 Thu Apr 28 23:06:14 2022