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md_0_1_Version 2019.3.log
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:-) GROMACS - gmx mdrun, 2019.3 (-:
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
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) 2001-2018, 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 2019.3
Executable: /shared/ucl/apps/gromacs/2019.3/intel-2018/bin/gmx
Data prefix: /shared/ucl/apps/gromacs/2019.3/intel-2018
Working dir: /lustre/scratch/scratch/ucbechz/20200109_Nuria_pH_MD/pH3.5_300K/repeat1
Process ID: 394759
Command line:
gmx mdrun -deffnm md_0_1 -cpi -append
GROMACS version: 2019.3
Precision: single
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support: disabled
SIMD instructions: AVX_512
FFT library: Intel MKL
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: disabled
Tracing support: disabled
C compiler: /shared/ucl/apps/intel/2018.Update3/compilers_and_libraries_2018.3.222/linux/bin/intel64/icc Intel 18.0.3.20180410
C compiler flags: -xCORE-AVX512 -qopt-zmm-usage=high -mkl=sequential -std=gnu99 -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits
C++ compiler: /shared/ucl/apps/intel/2018.Update3/compilers_and_libraries_2018.3.222/linux/bin/intel64/icpc Intel 18.0.3.20180410
C++ compiler flags: -xCORE-AVX512 -qopt-zmm-usage=high -mkl=sequential -std=c++11 -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits
Running on 1 node with total 36 cores, 36 logical cores
Hardware detected:
CPU info:
Vendor: Intel
Brand: Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz
Family: 6 Model: 85 Stepping: 7
Features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl 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: Only logical processor count
++++ 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.3243833
-------- -------- --- Thank You --- -------- --------
Non-default thread affinity set, disabling internal thread affinity
Input Parameters:
integrator = md
tinit = 0
dt = 0.002
nsteps = 1000000000000
init-step = 0
simulation-part = 1
comm-mode = Linear
nstcomm = 100
bd-fric = 0
ld-seed = 1974013184
emtol = 10
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
rtpi = 0.05
nstxout = 50000
nstvout = 0
nstfout = 0
nstlog = 50000
nstcalcenergy = 100
nstenergy = 50000
nstxout-compressed = 50000
compressed-x-precision = 1000
cutoff-scheme = Verlet
nstlist = 10
ns-type = Grid
pbc = xyz
periodic-molecules = false
verlet-buffer-tolerance = 0.005
rlist = 1
coulombtype = PME
coulomb-modifier = Potential-shift
rcoulomb-switch = 0
rcoulomb = 1
epsilon-r = 1
epsilon-rf = inf
vdw-type = Cut-off
vdw-modifier = Potential-shift
rvdw-switch = 0
rvdw = 1
DispCorr = EnerPres
table-extension = 1
fourierspacing = 0.16
fourier-nx = 72
fourier-ny = 72
fourier-nz = 72
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 = 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
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
grpopts:
nrdf: 13160.8 222576
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 10 to 50, rlist from 1 to 1.116
Initializing Domain Decomposition on 36 ranks
Dynamic load balancing: locked
Minimum cell size due to atom displacement: 0.479 nm
Initial maximum distances in bonded interactions:
two-body bonded interactions: 0.454 nm, LJ-14, atoms 3576 4713
multi-body bonded interactions: 0.454 nm, Ryckaert-Bell., atoms 3576 4713
Minimum cell size due to bonded interactions: 0.499 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.872 nm
Estimated maximum distance required for P-LINCS: 0.872 nm
This distance will limit the DD cell size, you can override this with -rcon
Guess for relative PME load: 0.24
Will use 27 particle-particle and 9 PME only ranks
This is a guess, check the performance at the end of the log file
Using 9 separate PME ranks, as guessed by mdrun
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 27 cells with a minimum initial size of 1.089 nm
The maximum allowed number of cells is: X 9 Y 9 Z 9
Domain decomposition grid 3 x 3 x 3, separate PME ranks 9
PME domain decomposition: 3 x 3 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 1 Y 1 Z 1
The initial domain decomposition cell size is: X 3.51 nm Y 3.51 nm Z 3.51 nm
The maximum allowed distance for atoms involved in interactions is:
non-bonded interactions 1.116 nm
(the following are initial values, they could change due to box deformation)
two-body bonded interactions (-rdd) 1.116 nm
multi-body bonded interactions (-rdd) 1.116 nm
atoms separated by up to 5 constraints (-rcon) 3.511 nm
When dynamic load balancing gets turned on, these settings will change to:
The maximum number of communication pulses is: X 1 Y 1 Z 1
The minimum size for domain decomposition cells is 1.116 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: X 0.32 Y 0.32 Z 0.32
The maximum allowed distance for atoms involved in interactions is:
non-bonded interactions 1.116 nm
two-body bonded interactions (-rdd) 1.116 nm
multi-body bonded interactions (-rdd) 1.116 nm
atoms separated by up to 5 constraints (-rcon) 1.116 nm
Using 36 MPI threads
Using 1 OpenMP thread per tMPI 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 0.320163 nm for Ewald
Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e+00, Ewald -1.000e-05
Initialized non-bonded Ewald correction tables, spacing: 9.33e-04 size: 1073
Long Range LJ corr.: <C6> 3.1893e-04
Generated table with 1058 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 1058 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 1058 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 1058 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1058 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1058 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 50 steps, buffer 0.116 nm, rlist 1.116 nm
inner list: updated every 12 steps, buffer 0.003 nm, rlist 1.003 nm
At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
outer list: updated every 50 steps, buffer 0.245 nm, rlist 1.245 nm
inner list: updated every 12 steps, buffer 0.048 nm, rlist 1.048 nm
Using geometric Lennard-Jones combination rule
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 6705
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 --- -------- --------
Linking all bonded interactions to atoms
Intra-simulation communication will occur every 10 steps.
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest
++++ 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: 117860 Atoms
Atom distribution over 27 domains: av 4365 stddev 75 min 4289 max 4626
Started mdrun on rank 0 Sun Jan 12 22:47:52 2020
Step Time
0 0.00000
Energies (kJ/mol)
Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
1.31131e+04 7.43495e+02 6.17820e+03 9.77778e+03 5.15413e+04
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
3.28241e+05 -1.58634e+04 -2.24237e+06 1.06330e+04 -1.83800e+06
Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
2.93000e+05 -1.54500e+06 -1.54493e+06 2.98976e+02 -2.25711e+02
Pressure (bar) Constr. rmsd
1.60558e+02 2.70869e-05
DD step 49 load imb.: force 8.4% pme mesh/force 6.499
step 200: timed with pme grid 72 72 72, coulomb cutoff 1.000: 76943.9 M-cycles
step 300: timed with pme grid 60 60 60, coulomb cutoff 1.097: 74549.8 M-cycles
step 400: timed with pme grid 52 52 52, coulomb cutoff 1.266: 69475.3 M-cycles
step 500: timed with pme grid 48 48 48, coulomb cutoff 1.371: 75426.3 M-cycles
step 600: timed with pme grid 44 44 44, coulomb cutoff 1.496: 70369.5 M-cycles
step 600: the maximum allowed grid scaling limits the PME load balancing to a coulomb cut-off of 1.496
step 700: timed with pme grid 44 44 44, coulomb cutoff 1.496: 70898.9 M-cycles
step 800: timed with pme grid 48 48 48, coulomb cutoff 1.371: 74619.2 M-cycles
step 900: timed with pme grid 52 52 52, coulomb cutoff 1.266: 76903.7 M-cycles
step 1000: timed with pme grid 56 56 56, coulomb cutoff 1.176: 72415.7 M-cycles
step 1100: timed with pme grid 60 60 60, coulomb cutoff 1.097: 75666.9 M-cycles
step 1200: timed with pme grid 64 64 64, coulomb cutoff 1.029: 69363.8 M-cycles
Writing checkpoint, step 1200 at Sun Jan 12 23:03:38 2020
step 1300: timed with pme grid 72 72 72, coulomb cutoff 1.000: 70603.2 M-cycles
step 1400: timed with pme grid 44 44 44, coulomb cutoff 1.496: 71869.4 M-cycles
step 1500: timed with pme grid 48 48 48, coulomb cutoff 1.371: 70901.5 M-cycles
step 1600: timed with pme grid 52 52 52, coulomb cutoff 1.266: 75311.6 M-cycles
step 1700: timed with pme grid 56 56 56, coulomb cutoff 1.176: 69372.0 M-cycles
step 1800: timed with pme grid 60 60 60, coulomb cutoff 1.097: 74317.0 M-cycles
step 1900: timed with pme grid 64 64 64, coulomb cutoff 1.029: 75613.9 M-cycles
step 2000: timed with pme grid 72 72 72, coulomb cutoff 1.000: 71775.7 M-cycles
step 2100: timed with pme grid 44 44 44, coulomb cutoff 1.496: 71810.6 M-cycles
step 2200: timed with pme grid 48 48 48, coulomb cutoff 1.371: 70568.2 M-cycles
step 2300: timed with pme grid 52 52 52, coulomb cutoff 1.266: 76071.2 M-cycles
Writing checkpoint, step 2350 at Sun Jan 12 23:18:19 2020
step 2400: timed with pme grid 56 56 56, coulomb cutoff 1.176: 74243.9 M-cycles
step 2500: timed with pme grid 60 60 60, coulomb cutoff 1.097: 71946.7 M-cycles
step 2600: timed with pme grid 64 64 64, coulomb cutoff 1.029: 70713.2 M-cycles
step 2700: timed with pme grid 72 72 72, coulomb cutoff 1.000: 72090.1 M-cycles
step 2800: timed with pme grid 44 44 44, coulomb cutoff 1.496: 73036.8 M-cycles
step 2900: timed with pme grid 48 48 48, coulomb cutoff 1.371: 71808.8 M-cycles
step 3000: timed with pme grid 52 52 52, coulomb cutoff 1.266: 78947.9 M-cycles
step 3100: timed with pme grid 56 56 56, coulomb cutoff 1.176: 72531.1 M-cycles
step 3200: timed with pme grid 60 60 60, coulomb cutoff 1.097: 68274.7 M-cycles
step 3300: timed with pme grid 64 64 64, coulomb cutoff 1.029: 74340.8 M-cycles
step 3400: timed with pme grid 72 72 72, coulomb cutoff 1.000: 71690.1 M-cycles
step 3500: timed with pme grid 44 44 44, coulomb cutoff 1.496: 70439.2 M-cycles
Writing checkpoint, step 3500 at Sun Jan 12 23:33:12 2020
-----------------------------------------------------------
Restarting from checkpoint, appending to previous log file.
:-) GROMACS - gmx mdrun, 2019.3 (-:
Executable: /shared/ucl/apps/gromacs/2019.3/intel-2018/bin/gmx
Data prefix: /shared/ucl/apps/gromacs/2019.3/intel-2018
Working dir: /lustre/scratch/scratch/ucbechz/20200109_Nuria_pH_MD/pH3.5_300K/repeat1
Process ID: 377676
Command line:
gmx mdrun -deffnm md_0_1 -cpi -append
GROMACS version: 2019.3
Precision: single
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support: disabled
SIMD instructions: AVX_512
FFT library: Intel MKL
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: disabled
Tracing support: disabled
C compiler: /shared/ucl/apps/intel/2018.Update3/compilers_and_libraries_2018.3.222/linux/bin/intel64/icc Intel 18.0.3.20180410
C compiler flags: -xCORE-AVX512 -qopt-zmm-usage=high -mkl=sequential -std=gnu99 -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits
C++ compiler: /shared/ucl/apps/intel/2018.Update3/compilers_and_libraries_2018.3.222/linux/bin/intel64/icpc Intel 18.0.3.20180410
C++ compiler flags: -xCORE-AVX512 -qopt-zmm-usage=high -mkl=sequential -std=c++11 -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits
Changing nstlist from 10 to 50, rlist from 1 to 1.116
Initializing Domain Decomposition on 36 ranks
Dynamic load balancing: locked
Minimum cell size due to atom displacement: 0.479 nm
Initial maximum distances in bonded interactions:
two-body bonded interactions: 0.453 nm, LJ-14, atoms 3576 4713
multi-body bonded interactions: 0.453 nm, Ryckaert-Bell., atoms 3576 4713
Minimum cell size due to bonded interactions: 0.499 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.872 nm
Estimated maximum distance required for P-LINCS: 0.872 nm
This distance will limit the DD cell size, you can override this with -rcon
Guess for relative PME load: 0.24
Will use 27 particle-particle and 9 PME only ranks
This is a guess, check the performance at the end of the log file
Using 9 separate PME ranks, as guessed by mdrun
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 27 cells with a minimum initial size of 1.089 nm
The maximum allowed number of cells is: X 9 Y 9 Z 9
Domain decomposition grid 3 x 3 x 3, separate PME ranks 9
PME domain decomposition: 3 x 3 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 1 Y 1 Z 1
The initial domain decomposition cell size is: X 3.51 nm Y 3.51 nm Z 3.51 nm
The maximum allowed distance for atoms involved in interactions is:
non-bonded interactions 1.116 nm
(the following are initial values, they could change due to box deformation)
two-body bonded interactions (-rdd) 1.116 nm
multi-body bonded interactions (-rdd) 1.116 nm
atoms separated by up to 5 constraints (-rcon) 3.511 nm
When dynamic load balancing gets turned on, these settings will change to:
The maximum number of communication pulses is: X 1 Y 1 Z 1
The minimum size for domain decomposition cells is 1.116 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: X 0.32 Y 0.32 Z 0.32
The maximum allowed distance for atoms involved in interactions is:
non-bonded interactions 1.116 nm
two-body bonded interactions (-rdd) 1.116 nm
multi-body bonded interactions (-rdd) 1.116 nm
atoms separated by up to 5 constraints (-rcon) 1.116 nm
Using 36 MPI threads
Using 1 OpenMP thread per tMPI 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 0.320163 nm for Ewald
Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e+00, Ewald -1.000e-05
Initialized non-bonded Ewald correction tables, spacing: 9.33e-04 size: 1073
Long Range LJ corr.: <C6> 3.1893e-04
Generated table with 1058 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 1058 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 1058 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 1058 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1058 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1058 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 50 steps, buffer 0.116 nm, rlist 1.116 nm
inner list: updated every 12 steps, buffer 0.003 nm, rlist 1.003 nm
At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
outer list: updated every 50 steps, buffer 0.245 nm, rlist 1.245 nm
inner list: updated every 12 steps, buffer 0.048 nm, rlist 1.048 nm
Using geometric Lennard-Jones combination rule
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 6705
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 --- -------- --------
Linking all bonded interactions to atoms
Intra-simulation communication will occur every 10 steps.
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest
There are: 117860 Atoms
Atom distribution over 27 domains: av 4365 stddev 67 min 4290 max 4586
Started mdrun on rank 0 Sun Jan 12 23:50:25 2020
DD step 3549 load imb.: force 6.0% pme mesh/force 6.942
step 3700: timed with pme grid 72 72 72, coulomb cutoff 1.000: 73078.8 M-cycles
step 3800: timed with pme grid 60 60 60, coulomb cutoff 1.097: 76004.1 M-cycles
step 3900: timed with pme grid 52 52 52, coulomb cutoff 1.266: 73763.1 M-cycles
step 4000: timed with pme grid 48 48 48, coulomb cutoff 1.372: 75023.7 M-cycles
step 4100: timed with pme grid 44 44 44, coulomb cutoff 1.496: 72166.1 M-cycles
step 4100: the maximum allowed grid scaling limits the PME load balancing to a coulomb cut-off of 1.496
step 4200: timed with pme grid 44 44 44, coulomb cutoff 1.496: 75198.5 M-cycles
step 4300: timed with pme grid 48 48 48, coulomb cutoff 1.372: 72129.2 M-cycles
step 4400: timed with pme grid 52 52 52, coulomb cutoff 1.266: 76468.6 M-cycles
step 4500: timed with pme grid 56 56 56, coulomb cutoff 1.176: 76771.2 M-cycles
step 4600: timed with pme grid 60 60 60, coulomb cutoff 1.097: 76239.8 M-cycles
step 4700: timed with pme grid 64 64 64, coulomb cutoff 1.029: 68403.5 M-cycles
Writing checkpoint, step 4700 at Mon Jan 13 00:06:10 2020
step 4800: timed with pme grid 72 72 72, coulomb cutoff 1.000: 74851.8 M-cycles
step 4900: timed with pme grid 44 44 44, coulomb cutoff 1.496: 71816.9 M-cycles
step 5000: timed with pme grid 48 48 48, coulomb cutoff 1.372: 70067.1 M-cycles
step 5100: timed with pme grid 52 52 52, coulomb cutoff 1.266: 75063.2 M-cycles
step 5200: timed with pme grid 56 56 56, coulomb cutoff 1.176: 67746.1 M-cycles
step 5300: timed with pme grid 60 60 60, coulomb cutoff 1.097: 74858.8 M-cycles
step 5400: timed with pme grid 64 64 64, coulomb cutoff 1.029: 73627.0 M-cycles
step 5500: timed with pme grid 72 72 72, coulomb cutoff 1.000: 70956.0 M-cycles
step 5600: timed with pme grid 44 44 44, coulomb cutoff 1.496: 72184.1 M-cycles
step 5700: timed with pme grid 48 48 48, coulomb cutoff 1.372: 69832.0 M-cycles
step 5800: timed with pme grid 52 52 52, coulomb cutoff 1.266: 76203.2 M-cycles
Writing checkpoint, step 5850 at Mon Jan 13 00:20:44 2020
step 5900: timed with pme grid 56 56 56, coulomb cutoff 1.176: 80353.0 M-cycles
step 6000: timed with pme grid 60 60 60, coulomb cutoff 1.097: 71679.5 M-cycles
step 6100: timed with pme grid 64 64 64, coulomb cutoff 1.029: 69680.1 M-cycles
step 6200: timed with pme grid 72 72 72, coulomb cutoff 1.000: 72512.0 M-cycles
step 6300: timed with pme grid 44 44 44, coulomb cutoff 1.496: 70126.0 M-cycles
step 6400: timed with pme grid 48 48 48, coulomb cutoff 1.372: 67307.0 M-cycles
step 6500: timed with pme grid 52 52 52, coulomb cutoff 1.266: 71516.5 M-cycles
step 6600: timed with pme grid 56 56 56, coulomb cutoff 1.176: 73730.9 M-cycles
step 6700: timed with pme grid 60 60 60, coulomb cutoff 1.097: 68960.4 M-cycles
step 6800: timed with pme grid 64 64 64, coulomb cutoff 1.029: 70300.4 M-cycles
step 6900: timed with pme grid 72 72 72, coulomb cutoff 1.000: 68042.5 M-cycles
step 7000: timed with pme grid 44 44 44, coulomb cutoff 1.496: 66444.8 M-cycles
Writing checkpoint, step 7050 at Mon Jan 13 00:35:42 2020
-----------------------------------------------------------
Restarting from checkpoint, appending to previous log file.
:-) GROMACS - gmx mdrun, 2019.3 (-:
Executable: /shared/ucl/apps/gromacs/2019.3/intel-2018/bin/gmx
Data prefix: /shared/ucl/apps/gromacs/2019.3/intel-2018
Working dir: /lustre/scratch/scratch/ucbechz/20200109_Nuria_pH_MD/pH3.5_300K/repeat1
Process ID: 441177
Command line:
gmx mdrun -deffnm md_0_1 -cpi -append
GROMACS version: 2019.3
Precision: single
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support: disabled
SIMD instructions: AVX_512
FFT library: Intel MKL
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: disabled
Tracing support: disabled
C compiler: /shared/ucl/apps/intel/2018.Update3/compilers_and_libraries_2018.3.222/linux/bin/intel64/icc Intel 18.0.3.20180410
C compiler flags: -xCORE-AVX512 -qopt-zmm-usage=high -mkl=sequential -std=gnu99 -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits
C++ compiler: /shared/ucl/apps/intel/2018.Update3/compilers_and_libraries_2018.3.222/linux/bin/intel64/icpc Intel 18.0.3.20180410
C++ compiler flags: -xCORE-AVX512 -qopt-zmm-usage=high -mkl=sequential -std=c++11 -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits
Changing nstlist from 10 to 50, rlist from 1 to 1.116
Initializing Domain Decomposition on 36 ranks
Dynamic load balancing: locked
Minimum cell size due to atom displacement: 0.479 nm
Initial maximum distances in bonded interactions:
two-body bonded interactions: 0.460 nm, LJ-14, atoms 321 1323
multi-body bonded interactions: 0.460 nm, Ryckaert-Bell., atoms 321 1323
Minimum cell size due to bonded interactions: 0.506 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.872 nm
Estimated maximum distance required for P-LINCS: 0.872 nm
This distance will limit the DD cell size, you can override this with -rcon
Guess for relative PME load: 0.24
Will use 27 particle-particle and 9 PME only ranks
This is a guess, check the performance at the end of the log file
Using 9 separate PME ranks, as guessed by mdrun
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 27 cells with a minimum initial size of 1.089 nm
The maximum allowed number of cells is: X 9 Y 9 Z 9
Domain decomposition grid 3 x 3 x 3, separate PME ranks 9
PME domain decomposition: 3 x 3 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 1 Y 1 Z 1
The initial domain decomposition cell size is: X 3.51 nm Y 3.51 nm Z 3.51 nm
The maximum allowed distance for atoms involved in interactions is:
non-bonded interactions 1.116 nm
(the following are initial values, they could change due to box deformation)
two-body bonded interactions (-rdd) 1.116 nm
multi-body bonded interactions (-rdd) 1.116 nm
atoms separated by up to 5 constraints (-rcon) 3.512 nm
When dynamic load balancing gets turned on, these settings will change to:
The maximum number of communication pulses is: X 1 Y 1 Z 1
The minimum size for domain decomposition cells is 1.116 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: X 0.32 Y 0.32 Z 0.32
The maximum allowed distance for atoms involved in interactions is:
non-bonded interactions 1.116 nm
two-body bonded interactions (-rdd) 1.116 nm
multi-body bonded interactions (-rdd) 1.116 nm
atoms separated by up to 5 constraints (-rcon) 1.116 nm
Using 36 MPI threads
Using 1 OpenMP thread per tMPI 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 0.320163 nm for Ewald
Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e+00, Ewald -1.000e-05
Initialized non-bonded Ewald correction tables, spacing: 9.33e-04 size: 1073
Long Range LJ corr.: <C6> 3.1893e-04
Generated table with 1058 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 1058 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 1058 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 1058 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1058 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1058 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 50 steps, buffer 0.116 nm, rlist 1.116 nm
inner list: updated every 12 steps, buffer 0.003 nm, rlist 1.003 nm
At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
outer list: updated every 50 steps, buffer 0.245 nm, rlist 1.245 nm
inner list: updated every 12 steps, buffer 0.048 nm, rlist 1.048 nm
Using geometric Lennard-Jones combination rule
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 6705
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 --- -------- --------
Linking all bonded interactions to atoms
Intra-simulation communication will occur every 10 steps.
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest
There are: 117860 Atoms
Atom distribution over 27 domains: av 4365 stddev 65 min 4284 max 4551
Started mdrun on rank 0 Mon Jan 13 00:54:56 2020
DD step 7099 load imb.: force 5.5% pme mesh/force 3.168
step 7250: timed with pme grid 72 72 72, coulomb cutoff 1.000: 191272.1 M-cycles
step 7350: timed with pme grid 60 60 60, coulomb cutoff 1.098: 111535.2 M-cycles
step 7450: timed with pme grid 52 52 52, coulomb cutoff 1.266: 212975.8 M-cycles
step 7550: timed with pme grid 56 56 56, coulomb cutoff 1.176: 184353.8 M-cycles
Writing checkpoint, step 7550 at Mon Jan 13 01:11:30 2020
step 7650: timed with pme grid 60 60 60, coulomb cutoff 1.098: 145578.0 M-cycles
step 7750: timed with pme grid 64 64 64, coulomb cutoff 1.029: 225974.2 M-cycles
optimal pme grid 60 60 60, coulomb cutoff 1.098
Writing checkpoint, step 7950 at Mon Jan 13 01:25:47 2020
Writing checkpoint, step 8400 at Mon Jan 13 01:40:46 2020
-----------------------------------------------------------
Restarting from checkpoint, appending to previous log file.
:-) GROMACS - gmx mdrun, 2019.3 (-:
Executable: /shared/ucl/apps/gromacs/2019.3/intel-2018/bin/gmx
Data prefix: /shared/ucl/apps/gromacs/2019.3/intel-2018
Working dir: /lustre/scratch/scratch/ucbechz/20200109_Nuria_pH_MD/pH3.5_300K/repeat1
Process ID: 88414
Command line:
gmx mdrun -deffnm md_0_1 -cpi -append
GROMACS version: 2019.3
Precision: single
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support: disabled
SIMD instructions: AVX_512
FFT library: Intel MKL
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: disabled
Tracing support: disabled
C compiler: /shared/ucl/apps/intel/2018.Update3/compilers_and_libraries_2018.3.222/linux/bin/intel64/icc Intel 18.0.3.20180410
C compiler flags: -xCORE-AVX512 -qopt-zmm-usage=high -mkl=sequential -std=gnu99 -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits
C++ compiler: /shared/ucl/apps/intel/2018.Update3/compilers_and_libraries_2018.3.222/linux/bin/intel64/icpc Intel 18.0.3.20180410
C++ compiler flags: -xCORE-AVX512 -qopt-zmm-usage=high -mkl=sequential -std=c++11 -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits
Changing nstlist from 10 to 50, rlist from 1 to 1.116
Initializing Domain Decomposition on 36 ranks
Dynamic load balancing: locked
Minimum cell size due to atom displacement: 0.479 nm
Initial maximum distances in bonded interactions:
two-body bonded interactions: 0.455 nm, LJ-14, atoms 3581 4708
multi-body bonded interactions: 0.455 nm, Ryckaert-Bell., atoms 4708 3581
Minimum cell size due to bonded interactions: 0.501 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.872 nm
Estimated maximum distance required for P-LINCS: 0.872 nm
This distance will limit the DD cell size, you can override this with -rcon
Guess for relative PME load: 0.24
Will use 27 particle-particle and 9 PME only ranks
This is a guess, check the performance at the end of the log file
Using 9 separate PME ranks, as guessed by mdrun
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 27 cells with a minimum initial size of 1.089 nm
The maximum allowed number of cells is: X 9 Y 9 Z 9
Domain decomposition grid 3 x 3 x 3, separate PME ranks 9
PME domain decomposition: 3 x 3 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 1 Y 1 Z 1
The initial domain decomposition cell size is: X 3.51 nm Y 3.51 nm Z 3.51 nm
The maximum allowed distance for atoms involved in interactions is:
non-bonded interactions 1.116 nm
(the following are initial values, they could change due to box deformation)
two-body bonded interactions (-rdd) 1.116 nm
multi-body bonded interactions (-rdd) 1.116 nm
atoms separated by up to 5 constraints (-rcon) 3.515 nm
When dynamic load balancing gets turned on, these settings will change to:
The maximum number of communication pulses is: X 1 Y 1 Z 1
The minimum size for domain decomposition cells is 1.116 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: X 0.32 Y 0.32 Z 0.32
The maximum allowed distance for atoms involved in interactions is:
non-bonded interactions 1.116 nm
two-body bonded interactions (-rdd) 1.116 nm
multi-body bonded interactions (-rdd) 1.116 nm
atoms separated by up to 5 constraints (-rcon) 1.116 nm
Using 36 MPI threads
Using 1 OpenMP thread per tMPI 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 0.320163 nm for Ewald
Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e+00, Ewald -1.000e-05
Initialized non-bonded Ewald correction tables, spacing: 9.33e-04 size: 1073
Long Range LJ corr.: <C6> 3.1893e-04
Generated table with 1058 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 1058 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 1058 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 1058 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1058 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1058 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 50 steps, buffer 0.116 nm, rlist 1.116 nm
inner list: updated every 12 steps, buffer 0.003 nm, rlist 1.003 nm
At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
outer list: updated every 50 steps, buffer 0.245 nm, rlist 1.245 nm
inner list: updated every 12 steps, buffer 0.048 nm, rlist 1.048 nm
Using geometric Lennard-Jones combination rule
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
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The number of constraints is 6705
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 --- -------- --------
Linking all bonded interactions to atoms
Intra-simulation communication will occur every 10 steps.
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest
There are: 117860 Atoms
Atom distribution over 27 domains: av 4365 stddev 67 min 4297 max 4589
Started mdrun on rank 0 Mon Jan 13 01:57:47 2020
DD step 8449 load imb.: force 7.2% pme mesh/force 5.050
step 8600: timed with pme grid 72 72 72, coulomb cutoff 1.000: 182431.3 M-cycles
step 8700: timed with pme grid 60 60 60, coulomb cutoff 1.098: 211861.9 M-cycles
step 8800: timed with pme grid 64 64 64, coulomb cutoff 1.030: 174691.1 M-cycles
Writing checkpoint, step 8800 at Mon Jan 13 02:13:38 2020
step 8900: timed with pme grid 72 72 72, coulomb cutoff 1.000: 212093.8 M-cycles
optimal pme grid 64 64 64, coulomb cutoff 1.030