You can not select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
727 lines
30 KiB
727 lines
30 KiB
2 years ago
|
:-) 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
|
||
|
|
|