There were no logged errors or warnings. Non-FAH system load was nominal. Kernel scheduler settings were typical for my system (all cores running nice 19 with SCHED_BATCH). The WU was not stalling, it was just going abnormally slowly, with only 100 steps between each 5 minute checkpoint:
Code: Select all
Writing checkpoint, step 1000200 at Sat Mar 29 05:59:40 2025
Writing checkpoint, step 1000300 at Sat Mar 29 06:03:56 2025
Writing checkpoint, step 1000400 at Sat Mar 29 06:08:12 2025
Writing checkpoint, step 1000500 at Sat Mar 29 06:12:29 2025
Writing checkpoint, step 1000600 at Sat Mar 29 06:16:45 2025
Writing checkpoint, step 1000800 at Sat Mar 29 06:25:17 2025
Code: Select all
:-) GROMACS - GROMACS, 2020.5-dev-20210116-ddc6077-unknown (-:
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: GROMACS, version 2020.5-dev-20210116-ddc6077-unknown
Working dir: /var/lib/fah-client/work/K1FPyoybdRldicNw6V7jsSBZoG7kU9WZE8a-7WHeCLg/01
Process ID: 1171779
GROMACS version: 2020.5-dev-20210116-ddc6077-unknown
GIT SHA1 hash: ddc6077cfc91185b44cf253801548ae5d6c5e673
Branched from: unknown
Precision: single
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
RDTSCP usage: disabled
TNG support: enabled
Hwloc support: disabled
Tracing support: disabled
C compiler: /usr/bin/x86_64-linux-gnu-gcc GNU 8.3.0
C compiler flags: -mavx2 -mfma -Wall -Wno-unused -Wunused-value -Wunused-parameter -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wundef -Werror=stringop-truncation -fexcess-precision=fast -funroll-all-loops -Wno-array-bounds -O3 -DNDEBUG
C++ compiler: /usr/bin/x86_64-linux-gnu-g++ GNU 8.3.0
C++ compiler flags: -mavx2 -mfma -Wall -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wmissing-declarations -Wundef -Wstringop-truncation -fexcess-precision=fast -funroll-all-loops -Wno-array-bounds -fopenmp -O3 -DNDEBUG
Note: 16 CPUs configured, but only 8 were detected to be online.
X86 Hyperthreading is likely disabled; enable it for better performance.
Running on 1 node with total 8 cores, 8 logical cores
Hardware detected:
CPU info:
Vendor: AMD
Brand: AMD Ryzen 7 7840U w/ Radeon 780M Graphics
Family: 25 Model: 116 Stepping: 1
Features: aes amd apic avx avx2 avx512f avx512cd avx512bw avx512vl clfsh cmov cx8 cx16 f16c fma htt lahf misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4a sse4.1 sse4.2 ssse3 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] [ 1] [ 2] [ 3] [ 4] [ 5] [ 6] [ 7]
The current CPU can measure timings more accurately than the code in
GROMACS was configured to use. This might affect your simulation
speed as accurate timings are needed for load-balancing.
Please consider rebuilding GROMACS 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 --- -------- --------
++++ PLEASE CITE THE DOI FOR THIS VERSION OF GROMACS ++++
https://doi.org/10.5281/zenodo.4420785
-------- -------- --- Thank You --- -------- --------
This run will default to '-update gpu' as requested by the GMX_FORCE_UPDATE_DEFAULT_GPU environment variable. GPU update with domain decomposition lacks substantial testing and should be used with caution.
Input Parameters:
integrator = sd
tinit = 0
dt = 0.002
nsteps = 500000
init-step = 1000000
simulation-part = 1
comm-mode = Linear
nstcomm = 100
bd-fric = 0
ld-seed = 1074724025
emtol = 10
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
rtpi = 0.05
nstxout = 5000
nstvout = 5000
nstfout = 0
nstlog = 5000
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 = 1
coulombtype = PME
coulomb-modifier = Potential-shift
rcoulomb-switch = 0
rcoulomb = 1
epsilon-r = 1
epsilon-rf = inf
vdw-type = PME
vdw-modifier = Potential-shift
rvdw-switch = 0
rvdw = 1
DispCorr = EnerPres
table-extension = 1
fourierspacing = 0.1
fourier-nx = 112
fourier-ny = 112
fourier-nz = 112
pme-order = 6
ewald-rtol = 1e-06
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 = Parrinello-Rahman
pcoupltype = Isotropic
nstpcouple = 10
tau-p = 0.5
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 = All
posres-com (3):
posres-com[0]= 0.00000e+00
posres-com[1]= 0.00000e+00
posres-com[2]= 0.00000e+00
posres-comB (3):
posres-comB[0]= 0.00000e+00
posres-comB[1]= 0.00000e+00
posres-comB[2]= 0.00000e+00
QMMM = false
QMconstraints = 0
QMMMscheme = 0
MMChargeScaleFactor = 1
qm-opts:
ngQM = 0
constraint-algorithm = Lincs
continuation = false
Shake-SOR = false
shake-tol = 0.0001
lincs-order = 4
lincs-iter = 1
lincs-warnangle = 30
nwall = 0
wall-type = 9-3
wall-r-linpot = -1
wall-atomtype[0] = -1
wall-atomtype[1] = -1
wall-density[0] = 0
wall-density[1] = 0
wall-ewald-zfac = 3
pull = false
awh = false
rotation = false
interactiveMD = false
disre = No
disre-weighting = Conservative
disre-mixed = false
dr-fc = 1000
dr-tau = 0
nstdisreout = 100
orire-fc = 0
orire-tau = 0
nstorireout = 100
free-energy = yes
init-lambda = -1
init-lambda-state = 7
delta-lambda = 0
nstdhdl = 500
n-lambdas = 21
separate-dvdl:
fep-lambdas = TRUE
mass-lambdas = FALSE
coul-lambdas = FALSE
vdw-lambdas = FALSE
bonded-lambdas = FALSE
restraint-lambdas = FALSE
temperature-lambdas = FALSE
all-lambdas:
fep-lambdas = 0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1
mass-lambdas = 0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1
coul-lambdas = 0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1
vdw-lambdas = 0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1
bonded-lambdas = 0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1
restraint-lambdas = 0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1
temperature-lambdas = 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
calc-lambda-neighbors = -1
dhdl-print-energy = potential
sc-alpha = 0.5
sc-power = 1
sc-r-power = 6
sc-sigma = 0.3
sc-sigma-min = 0.3
sc-coul = true
dh-hist-size = 0
dh-hist-spacing = 0.1
separate-dhdl-file = yes
dhdl-derivatives = yes
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: 194266
ref-t: 300
tau-t: 1
annealing: No
annealing-npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp-flags[ 0]: 0
Changing nstlist from 10 to 100, rlist from 1 to 1.005
Update task on the GPU was required, by the GMX_FORCE_UPDATE_DEFAULT_GPU environment variable, but the following condition(s) were not satisfied:
Either PME or short-ranged non-bonded interaction tasks must run on the GPU.
Compatible GPUs must have been found.
Only a CUDA build is supported.
Only the md integrator is supported.
Free energy perturbations are not supported.
The number of coupled constraints is higher than supported in the CUDA LINCS code.
Will use CPU version of update.
Using 1 MPI thread
Non-default thread affinity set, disabling internal thread affinity
Using 7 OpenMP threads
System total charge, top. A: 0.003 top. B: 0.003
Will do PME sum in reciprocal space for LJ dispersion 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 0.298423 nm for LJ Ewald
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 0.289108 nm for Ewald
Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e-03, Ewald -1.000e-06
Initialized non-bonded Ewald tables, spacing: 8.87e-04 size: 1129
Using shifted Lennard-Jones, switch between 0 and 1 nm
Generated table with 1002 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1002 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1002 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Using SIMD 4x8 nonbonded short-range kernels
Using a 4x8 pair-list setup:
updated every 100 steps, buffer 0.005 nm, rlist 1.005 nm
At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
updated every 100 steps, buffer 0.182 nm, rlist 1.182 nm
Long Range LJ corr.: <C6> 1.1539e-06
There are 30 atoms and 30 charges for free energy perturbation
Removing pbc first time
Initializing LINear Constraint Solver
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
LINCS: A Linear Constraint Solver for molecular simulations
J. Comp. Chem. 18 (1997) pp. 1463-1472
-------- -------- --- Thank You --- -------- --------
The number of constraints is 8441
++++ 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 --- -------- --------
Setting the maximum number of constraint warnings to 2147483647
Initial vector of lambda components:[ 0.3500 0.3500 0.3500 0.3500 0.3500 0.3500 0.0000 ]
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
N. Goga and A. J. Rzepiela and A. H. de Vries and S. J. Marrink and H. J. C.
Berendsen
Efficient Algorithms for Langevin and DPD Dynamics
J. Chem. Theory Comput. 8 (2012) pp. 3637--3649
-------- -------- --- Thank You --- -------- --------
There are: 97101 Atoms
Constraining the starting coordinates (step 1000000)
Constraining the coordinates at t0-dt (step 1000000)
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest
RMS relative constraint deviation after constraining: 1.18e-05
Initial temperature: 300.691 K
Started mdrun on rank 0 Sat Mar 29 05:51:03 2025
Step Time
1000000 2000.00000
Energies (kJ/mol)
Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
1.76447e+04 2.13414e+04 1.09885e+03 9.23870e+03 7.56705e+04
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. LJ recip.
2.72786e+05 -4.66277e+01 -1.62509e+06 1.40961e+04 -1.13945e+05
Position Rest. Potential Kinetic En. Total Energy Temperature
5.84771e+02 -1.32662e+06 2.42798e+05 -1.08382e+06 3.00638e+02
Pres. DC (bar) Pressure (bar) dVremain/dl Constr. rmsd
-7.93814e-01 1.33210e+01 -2.64108e+01 1.24773e-05
Writing checkpoint, step 1000200 at Sat Mar 29 05:59:40 2025
Writing checkpoint, step 1000300 at Sat Mar 29 06:03:56 2025
Writing checkpoint, step 1000400 at Sat Mar 29 06:08:12 2025
Writing checkpoint, step 1000500 at Sat Mar 29 06:12:29 2025
Writing checkpoint, step 1000600 at Sat Mar 29 06:16:45 2025
Writing checkpoint, step 1000800 at Sat Mar 29 06:25:17 2025
Writing checkpoint, step 1000900 at Sat Mar 29 06:29:35 2025
Writing checkpoint, step 1001000 at Sat Mar 29 06:33:52 2025
Writing checkpoint, step 1001100 at Sat Mar 29 06:38:08 2025
Writing checkpoint, step 1001200 at Sat Mar 29 06:42:25 2025
Writing checkpoint, step 1001300 at Sat Mar 29 06:46:42 2025
Writing checkpoint, step 1001500 at Sat Mar 29 06:55:14 2025
Received the remote second INT/TERM signal, stopping within 11 steps
Writing checkpoint, step 1001600 at Sat Mar 29 06:59:35 2025
Step Time
1001601 2003.20200
Writing checkpoint, step 1001601 at Sat Mar 29 06:59:35 2025
Energies (kJ/mol)
Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
1.75208e+04 2.14735e+04 1.04005e+03 9.16521e+03 7.56769e+04
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. LJ recip.
2.72395e+05 -4.66524e+01 -1.62555e+06 1.41485e+04 -1.14005e+05
Position Rest. Potential Kinetic En. Total Energy Temperature
5.94462e+02 -1.32759e+06 2.42321e+05 -1.08527e+06 3.00047e+02
Pres. DC (bar) Pressure (bar) dVremain/dl Constr. rmsd
-7.94653e-01 -6.78620e+01 -2.45375e+02 1.26114e-05
<====== ############### ==>
<==== A V E R A G E S ====>
<== ############### ======>
Statistics over 1602 steps using 17 frames
Energies (kJ/mol)
Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
1.76182e+04 2.12718e+04 1.06178e+03 9.22057e+03 7.57611e+04
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. LJ recip.
2.72480e+05 -4.66669e+01 -1.62518e+06 1.40836e+04 -1.14061e+05
Position Rest. Potential Kinetic En. Total Energy Temperature
5.72261e+02 -1.32722e+06 2.42985e+05 -1.08424e+06 3.00870e+02
Pres. DC (bar) Pressure (bar) dVremain/dl Constr. rmsd
-7.95149e-01 -7.61378e+00 -1.97357e+02 0.00000e+00
Box-X Box-Y Box-Z
1.11331e+01 1.11331e+01 7.87228e+00
Total Virial (kJ/mol)
8.12369e+04 2.18138e+02 1.71726e+02
2.02617e+02 8.12812e+04 -1.02466e+03
1.45648e+02 -1.03797e+03 8.11494e+04
Pressure (bar)
-5.34530e+00 -7.05055e+00 -7.67331e+00
-6.52253e+00 -1.05447e+01 3.72356e+01
-6.78555e+00 3.76885e+01 -6.95129e+00
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
-----------------------------------------------------------------------------
NB Free energy kernel 6940.595124 6940.595 0.1
Pair Search distance check 590.133036 5311.197 0.1
NxN Ewald Elec. + LJ [F] 38401.295328 3916932.123 39.1
NxN Ewald Elec. + LJ [V&F] 436.338336 61087.367 0.6
NxN Ewald Elec. [F] 31024.658016 1892504.139 18.9
NxN Ewald Elec. [V&F] 352.533600 29612.822 0.3
1,4 nonbonded interactions 34.987080 3148.837 0.0
Calc Weights 466.667406 16800.027 0.2
Spread Q Bspline 134400.212928 268800.426 2.7
Gather F Bspline 134400.212928 806401.278 8.1
3D-FFT 367710.661296 2941685.290 29.4
Solve PME 80.381952 5144.445 0.1
Shift-X 1.650717 9.904 0.0
Angles 24.302340 4082.793 0.0
Propers 37.789980 8653.905 0.1
Impropers 2.899514 603.099 0.0
Pos. Restr. 0.828234 41.412 0.0
Virial 15.737652 283.278 0.0
Update 155.555802 4822.230 0.0
Stop-CM 1.747818 17.478 0.0
Calc-Ekin 31.363623 846.818 0.0
Lincs 27.061846 1623.711 0.0
Lincs-Mat 583.697184 2334.789 0.0
Constraint-V 338.047375 2704.379 0.0
Constraint-Vir 15.719508 377.268 0.0
Settle 94.676386 30580.473 0.3
-----------------------------------------------------------------------------
Total 10011350.083 100.0
-----------------------------------------------------------------------------
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, each using 7 OpenMP threads
Computing: Num Num Call Wall time Giga-Cycles
Ranks Threads Count (s) total sum %
-----------------------------------------------------------------------------
Neighbor search 1 7 17 7.075 163.126 0.2
Force 1 7 1602 513.627 11842.542 12.5
PME mesh 1 7 1602 2355.503 54310.088 57.3
NB X/F buffer ops. 1 7 3187 156.439 3606.976 3.8
Write traj. 1 7 15 15.038 346.728 0.4
Update 1 7 3204 155.958 3595.869 3.8
Constraints 1 7 3206 885.797 20423.541 21.5
Rest 22.828 526.327 0.6
-----------------------------------------------------------------------------
Total 4112.265 94815.196 100.0
-----------------------------------------------------------------------------
Breakdown of PME mesh computation
-----------------------------------------------------------------------------
PME spread 1 7 6408 737.530 17004.994 17.9
PME gather 1 7 6408 977.503 22537.982 23.8
PME 3D-FFT 1 7 12816 511.478 11792.995 12.4
PME solve LJ 1 7 3204 21.356 492.392 0.5
PME solve Elec 1 7 3204 2.848 65.668 0.1
-----------------------------------------------------------------------------
Core t (s) Wall t (s) (%)
Time: 28785.854 4112.265 700.0
1h08:32
(ns/day) (hour/ns)
Performance: 0.067 356.522
Finished mdrun on rank 0 Sat Mar 29 06:59:35 2025
Reading checkpoint file state.cpt
file generated by:
file generated at: Sat Mar 29 06:59:35 2025
GROMACS double prec.: 0
simulation part #: 1
step: 1001601
time: 2003.202000
-----------------------------------------------------------
Restarting from checkpoint, appending to previous log file.
:-) GROMACS - GROMACS, 2020.5-dev-20210116-ddc6077-unknown (-:
Working dir: /var/lib/fah-client/work/K1FPyoybdRldicNw6V7jsSBZoG7kU9WZE8a-7WHeCLg/01
Process ID: 1173903
GROMACS version: 2020.5-dev-20210116-ddc6077-unknown
GIT SHA1 hash: ddc6077cfc91185b44cf253801548ae5d6c5e673
Branched from: unknown
Precision: single
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
RDTSCP usage: disabled
TNG support: enabled
Hwloc support: disabled
Tracing support: disabled
C compiler: /usr/bin/x86_64-linux-gnu-gcc GNU 8.3.0
C compiler flags: -mavx2 -mfma -Wall -Wno-unused -Wunused-value -Wunused-parameter -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wundef -Werror=stringop-truncation -fexcess-precision=fast -funroll-all-loops -Wno-array-bounds -O3 -DNDEBUG
C++ compiler: /usr/bin/x86_64-linux-gnu-g++ GNU 8.3.0
C++ compiler flags: -mavx2 -mfma -Wall -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wmissing-declarations -Wundef -Wstringop-truncation -fexcess-precision=fast -funroll-all-loops -Wno-array-bounds -fopenmp -O3 -DNDEBUG
Changing nstlist from 10 to 100, rlist from 1 to 1.005
Update task on the GPU was required, by the GMX_FORCE_UPDATE_DEFAULT_GPU environment variable, but the following condition(s) were not satisfied:
Either PME or short-ranged non-bonded interaction tasks must run on the GPU.
Compatible GPUs must have been found.
Only a CUDA build is supported.
Only the md integrator is supported.
Free energy perturbations are not supported.
The number of coupled constraints is higher than supported in the CUDA LINCS code.
Will use CPU version of update.
Using 1 MPI thread
Non-default thread affinity set, disabling internal thread affinity
Using 7 OpenMP threads
System total charge, top. A: 0.003 top. B: 0.003
Will do PME sum in reciprocal space for LJ dispersion 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 0.298423 nm for LJ Ewald
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 0.289108 nm for Ewald
Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e-03, Ewald -1.000e-06
Initialized non-bonded Ewald tables, spacing: 8.87e-04 size: 1129
Using shifted Lennard-Jones, switch between 0 and 1 nm
Generated table with 1002 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1002 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1002 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Using SIMD 4x8 nonbonded short-range kernels
Using a 4x8 pair-list setup:
updated every 100 steps, buffer 0.005 nm, rlist 1.005 nm
At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
updated every 100 steps, buffer 0.182 nm, rlist 1.182 nm
Long Range LJ corr.: <C6> 1.1539e-06
There are 30 atoms and 30 charges for free energy perturbation
Initializing LINear Constraint Solver
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
LINCS: A Linear Constraint Solver for molecular simulations
J. Comp. Chem. 18 (1997) pp. 1463-1472
-------- -------- --- Thank You --- -------- --------
The number of constraints is 8441
++++ 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 --- -------- --------
Setting the maximum number of constraint warnings to 2147483647
Initial vector of lambda components:[ 0.3500 0.3500 0.3500 0.3500 0.3500 0.3500 0.0000 ]
There are: 97101 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 Sat Mar 29 06:59:43 2025
Step Time
1005000 2010.00000
Energies (kJ/mol)
Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
1.78943e+04 2.13561e+04 1.06903e+03 9.14452e+03 7.58080e+04
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. LJ recip.
2.73847e+05 -4.66621e+01 -1.62760e+06 1.42622e+04 -1.14060e+05
Position Rest. Potential Kinetic En. Total Energy Temperature
5.80356e+02 -1.32774e+06 2.42607e+05 -1.08514e+06 3.00402e+02
Pres. DC (bar) Pressure (bar) dVremain/dl Constr. rmsd
-7.94983e-01 1.29168e+01 -2.95358e+01 1.25638e-05
Writing checkpoint, step 1006700 at Sat Mar 29 07:04:47 2025
Step Time
1010000 2020.00000
Energies (kJ/mol)
Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
1.75239e+04 2.12665e+04 1.06937e+03 9.07527e+03 7.58257e+04
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. LJ recip.
2.71210e+05 -4.65080e+01 -1.62330e+06 1.40239e+04 -1.13690e+05
Position Rest. Potential Kinetic En. Total Energy Temperature
5.85316e+02 -1.32645e+06 2.43347e+05 -1.08311e+06 3.01318e+02
Pres. DC (bar) Pressure (bar) dVremain/dl Constr. rmsd
-7.89749e-01 -1.92865e+02 2.34520e+01 1.30552e-05
Writing checkpoint, step 1011700 at Sat Mar 29 07:09:45 2025
Step Time
1015000 2030.00000
Energies (kJ/mol)
Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
1.74927e+04 2.11825e+04 1.02925e+03 9.23814e+03 7.55764e+04
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. LJ recip.
2.73925e+05 -4.67688e+01 -1.62540e+06 1.41663e+04 -1.14268e+05
Position Rest. Potential Kinetic En. Total Energy Temperature
5.06469e+02 -1.32659e+06 2.42885e+05 -1.08371e+06 3.00745e+02
Pres. DC (bar) Pressure (bar) dVremain/dl Constr. rmsd
-7.98619e-01 2.29081e+01 5.73640e+01 1.26620e-05
Writing checkpoint, step 1016800 at Sat Mar 29 07:14:49 2025
Step Time
1020000 2040.00000
Energies (kJ/mol)
Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
1.76625e+04 2.14868e+04 1.11678e+03 9.26524e+03 7.58738e+04
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. LJ recip.
2.72403e+05 -4.68009e+01 -1.62767e+06 1.39312e+04 -1.14380e+05
Position Rest. Potential Kinetic En. Total Energy Temperature
6.27902e+02 -1.32973e+06 2.42966e+05 -1.08676e+06 3.00846e+02
Pres. DC (bar) Pressure (bar) dVremain/dl Constr. rmsd
-7.99715e-01 4.11403e+01 2.03969e+01 1.24796e-05
Writing checkpoint, step 1021800 at Sat Mar 29 07:19:47 2025
Received the remote second INT/TERM signal, stopping within 11 steps
Step Time
1023151 2046.30200
Writing checkpoint, step 1023151 at Sat Mar 29 07:21:08 2025
Energies (kJ/mol)
Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
1.78573e+04 2.11744e+04 1.02424e+03 9.19195e+03 7.56376e+04
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. LJ recip.
2.75515e+05 -4.65865e+01 -1.62846e+06 1.41853e+04 -1.13877e+05
Position Rest. Potential Kinetic En. Total Energy Temperature
5.35584e+02 -1.32727e+06 2.43462e+05 -1.08380e+06 3.01460e+02
Pres. DC (bar) Pressure (bar) dVremain/dl Constr. rmsd
-7.92412e-01 5.98015e+01 -2.00189e+02 1.27571e-05
<====== ############### ==>
<==== A V E R A G E S ====>
<== ############### ======>
Statistics over 23152 steps using 232 frames
Energies (kJ/mol)
Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
1.77403e+04 2.12862e+04 1.06869e+03 9.20593e+03 7.57173e+04
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. LJ recip.
2.72918e+05 -4.66662e+01 -1.62577e+06 1.41121e+04 -1.14047e+05
Position Rest. Potential Kinetic En. Total Energy Temperature
5.62726e+02 -1.32725e+06 2.42778e+05 -1.08447e+06 3.00613e+02
Pres. DC (bar) Pressure (bar) dVremain/dl Constr. rmsd
-7.95124e-01 5.53275e+00 -2.00526e+02 0.00000e+00
Box-X Box-Y Box-Z
1.11332e+01 1.11332e+01 7.87233e+00
Total Virial (kJ/mol)
8.11498e+04 -8.82006e+01 1.42992e+02
-8.71236e+01 8.07133e+04 -5.00858e+02
1.42483e+02 -5.02929e+02 8.04355e+04
Pressure (bar)
-5.90240e+00 3.44922e+00 -5.40251e+00
3.41217e+00 5.68858e+00 1.71956e+01
-5.38547e+00 1.72660e+01 1.68121e+01
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
-----------------------------------------------------------------------------
NB Free energy kernel 93131.058450 93131.058 0.1
Pair Search distance check 7496.126708 67465.140 0.1
NxN Ewald Elec. + LJ [F] 516921.322320 52725974.877 39.2
NxN Ewald Elec. + LJ [V&F] 5233.273568 732658.300 0.5
NxN Ewald Elec. [F] 417787.166544 25485017.159 18.9
NxN Ewald Elec. [V&F] 4229.592576 355285.776 0.3
1,4 nonbonded interactions 470.650072 42358.506 0.0
Calc Weights 6277.870953 226003.354 0.2
Spread Q Bspline 1808026.834464 3616053.669 2.7
Gather F Bspline 1808026.834464 10848161.007 8.1
3D-FFT 4946649.476648 39573195.813 29.4
Solve PME 1081.342976 69205.950 0.1
Shift-X 20.973816 125.843 0.0
Angles 326.928670 54924.017 0.0
Propers 508.340554 116409.987 0.1
Impropers 39.001841 8112.383 0.0
Pos. Restr. 11.141867 557.093 0.0
Virial 209.446776 3770.042 0.0
Update 2092.623651 64871.333 0.0
Stop-CM 20.876715 208.767 0.0
Calc-Ekin 418.602411 11302.265 0.0
Lincs 363.823982 21829.439 0.0
Lincs-Mat 7847.322528 31389.290 0.0
Constraint-V 4546.183450 36369.468 0.0
Constraint-Vir 209.205304 5020.927 0.0
Settle 1272.845162 411128.987 0.3
-----------------------------------------------------------------------------
Total 134600530.452 100.0
-----------------------------------------------------------------------------
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, each using 7 OpenMP threads
Computing: Num Num Call Wall time Giga-Cycles
Ranks Threads Count (s) total sum %
-----------------------------------------------------------------------------
Neighbor search 1 7 216 5.322 122.717 0.4
Force 1 7 21551 287.860 6637.087 22.4
PME mesh 1 7 21551 953.597 21986.779 74.2
NB X/F buffer ops. 1 7 42886 5.642 130.095 0.4
Write traj. 1 7 9 3.947 91.002 0.3
Update 1 7 43102 11.782 271.654 0.9
Constraints 1 7 43102 14.943 344.533 1.2
Rest 1.772 40.858 0.1
-----------------------------------------------------------------------------
Total 1284.865 29624.724 100.0
-----------------------------------------------------------------------------
Breakdown of PME mesh computation
-----------------------------------------------------------------------------
PME spread 1 7 86204 368.119 8487.602 28.7
PME gather 1 7 86204 316.352 7294.022 24.6
PME 3D-FFT 1 7 172408 225.141 5190.999 17.5
PME solve LJ 1 7 43102 34.150 787.390 2.7
PME solve Elec 1 7 43102 9.200 212.126 0.7
-----------------------------------------------------------------------------
Core t (s) Wall t (s) (%)
Time: 8994.054 1284.865 700.0
(ns/day) (hour/ns)
Performance: 2.898 8.281
Finished mdrun on rank 0 Sat Mar 29 07:21:08 2025