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|
:-) GROMACS - gmx mdrun, 2022-beta1-dev-20211123-c831d37c81 (double precision) (-:
GROMACS is written by:
Andrey Alekseenko Emile Apol Rossen Apostolov
Paul Bauer Herman J.C. Berendsen Par Bjelkmar
Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra
Oliver Fleetwood Gaurav Garg Gilles Gouaillardet
Alan Gray Gerrit Groenhof Anca Hamuraru
Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov
Christoph Junghans Joe Jordan Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner
Per Larsson Justin A. Lemkul Viveca Lindahl
Magnus Lundborg Erik Marklund Pascal Merz
Pieter Meulenhoff Teemu Murtola Szilard Pall
Sander Pronk Roland Schulz Michael Shirts
Alexey Shvetsov Alfons Sijbers Peter Tieleman
Jon Vincent Teemu Virolainen Christian Wennberg
Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx mdrun, version 2022-beta1-dev-20211123-c831d37c81 (double precision)
Executable: /home/mabraham/git/review/build-cmake-gcc-double-reference/install/bin/gmx_d
Data prefix: /home/mabraham/git/review/build-cmake-gcc-double-reference/install
Working dir: /home/mabraham/git/regressiontests/complex/pull_geometry_angle
Process ID: 237271
Command line:
gmx_d mdrun -notunepme
GROMACS version: 2022-beta1-dev-20211123-c831d37c81
GIT SHA1 hash: c831d37c8148f0af60cbc03ed7e35b7f5a20a9ae
Precision: double
Memory model: 64 bit
MPI library: none
OpenMP support: disabled
GPU support: disabled
SIMD instructions: NONE
CPU FFT library: fftpack (built-in)
GPU FFT library: none
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: hwloc-2.1.0
Tracing support: disabled
C compiler: /usr/bin/gcc-7 GNU 7.5.0
C compiler flags: -pthread -Wno-unknown-pragmas -Wall -Wno-unused -Wunused-value -Wunused-parameter -Wextra -Wno-sign-compare -Wpointer-arith -Wundef -Wno-missing-field-initializers -O0 -g
C++ compiler: /usr/bin/g++-7 GNU 7.5.0
C++ compiler flags: -pthread -Wno-unknown-pragmas -Wall -Wextra -Wpointer-arith -Wmissing-declarations -Wundef -Wno-missing-field-initializers -O0 -g
Running on 1 node with total 6 cores, 12 logical cores
Hardware detected:
CPU info:
Vendor: Intel
Brand: Intel(R) Core(TM) i7-10750H CPU @ 2.60GHz
Family: 6 Model: 165 Stepping: 2
Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
Hardware topology: Full, with devices
Sockets, cores, and logical processors:
Socket 0: [ 0 6] [ 1 7] [ 2 8] [ 3 9] [ 4 10] [ 5 11]
Numa nodes:
Node 0 (16515796992 bytes mem): 0 6 1 7 2 8 3 9 4 10 5 11
Latency:
0
0 1.00
Caches:
L1: 32768 bytes, linesize 64 bytes, assoc. 8, shared 2 ways
L2: 262144 bytes, linesize 64 bytes, assoc. 4, shared 2 ways
L3: 12582912 bytes, linesize 64 bytes, assoc. 16, shared 12 ways
PCI devices:
0000:01:00.0 Id: 10de:1f95 Class: 0x0302 Numa: 0
0000:00:02.0 Id: 8086:9bc4 Class: 0x0300 Numa: 0
0000:00:14.3 Id: 8086:06f0 Class: 0x0280 Numa: 0
0000:6d:00.0 Id: 1344:5405 Class: 0x0108 Numa: 0
Highest SIMD level supported by all nodes in run: AVX2_256
SIMD instructions selected at compile time: None
This program was compiled for different hardware than you are running on,
which could influence performance.
++++ 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 --- -------- --------
Input Parameters:
integrator = md
tinit = 0
dt = 0.002
nsteps = 20
init-step = 0
simulation-part = 1
mts = false
comm-mode = Linear
nstcomm = 10
bd-fric = 0
ld-seed = 1993
emtol = 10
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
rtpi = 0.05
nstxout = 20
nstvout = 1
nstfout = 1
nstlog = 0
nstcalcenergy = 1
nstenergy = 1
nstxout-compressed = 20
compressed-x-precision = 1000
cutoff-scheme = Verlet
nstlist = 10
pbc = xyz
periodic-molecules = false
verlet-buffer-tolerance = 0.005
rlist = 0.8
coulombtype = PME
coulomb-modifier = Potential-shift
rcoulomb-switch = 0
rcoulomb = 0.8
epsilon-r = 1
epsilon-rf = inf
vdw-type = Cut-off
vdw-modifier = Potential-shift
rvdw-switch = 0
rvdw = 0.8
DispCorr = EnerPres
table-extension = 1
fourierspacing = 0.13
fourier-nx = 24
fourier-ny = 24
fourier-nz = 24
pme-order = 4
ewald-rtol = 1e-06
ewald-rtol-lj = 0.001
lj-pme-comb-rule = Geometric
ewald-geometry = 3d
epsilon-surface = 0
tcoupl = V-rescale
nsttcouple = 10
nh-chain-length = 0
print-nose-hoover-chain-variables = false
pcoupl = No
pcoupltype = Isotropic
nstpcouple = -1
tau-p = 1
compressibility (3x3):
compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref-p (3x3):
ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
refcoord-scaling = No
posres-com (3):
posres-com[0]= 0.00000e+00
posres-com[1]= 0.00000e+00
posres-com[2]= 0.00000e+00
posres-comB (3):
posres-comB[0]= 0.00000e+00
posres-comB[1]= 0.00000e+00
posres-comB[2]= 0.00000e+00
QMMM = false
qm-opts:
ngQM = 0
constraint-algorithm = Lincs
continuation = 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 = true
pull-cylinder-r = 1.5
pull-constr-tol = 1e-06
pull-print-COM = false
pull-print-ref-value = false
pull-print-components = false
pull-nstxout = 50
pull-nstfout = 50
pull-pbc-ref-prev-step-com = false
pull-xout-average = false
pull-fout-average = false
pull-ngroups = 4
pull-group 0:
atom: not available
weight: not available
pbcatom = -1
pull-group 1:
atom (1):
atom[0]=8
weight: not available
pbcatom = -1
pull-group 2:
atom (1):
atom[0]=0
weight: not available
pbcatom = -1
pull-group 3:
atom (1):
atom[0]=18
weight: not available
pbcatom = -1
pull-ncoords = 1
pull-coord 0:
type = umbrella
geometry = angle
group[0] = 1
group[1] = 2
group[2] = 1
group[3] = 3
dim (3):
dim[0]=1
dim[1]=1
dim[2]=0
origin (3):
origin[0]= 0.00000e+00
origin[1]= 0.00000e+00
origin[2]= 0.00000e+00
vec (3):
vec[0]= 0.00000e+00
vec[1]= 0.00000e+00
vec[2]= 0.00000e+00
start = true
init = 130.396
rate = 1
k = 4000
kB = 4000
awh = false
rotation = false
interactiveMD = false
disre = No
disre-weighting = Conservative
disre-mixed = false
dr-fc = 1000
dr-tau = 0
nstdisreout = 100
orire-fc = 0
orire-tau = 0
nstorireout = 100
free-energy = no
cos-acceleration = 0
deform (3x3):
deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
simulated-tempering = false
swapcoords = no
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
applied-forces:
electric-field:
x:
E0 = 0
omega = 0
t0 = 0
sigma = 0
y:
E0 = 0
omega = 0
t0 = 0
sigma = 0
z:
E0 = 0
omega = 0
t0 = 0
sigma = 0
density-guided-simulation:
active = false
group = protein
similarity-measure = inner-product
atom-spreading-weight = unity
force-constant = 1e+09
gaussian-transform-spreading-width = 0.2
gaussian-transform-spreading-range-in-multiples-of-width = 4
reference-density-filename = reference.mrc
nst = 1
normalize-densities = true
adaptive-force-scaling = false
adaptive-force-scaling-time-constant = 4
shift-vector =
transformation-matrix =
qmmm-cp2k:
active = false
qmgroup = System
qmmethod = PBE
qmfilenames =
qmcharge = 0
qmmultiplicity = 1
grpopts:
nrdf: 51
ref-t: 310
tau-t: 0.1
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 0.8 to 0.8
Initializing Domain Decomposition on 1 ranks
Dynamic load balancing: auto
Using update groups, nr 10, average size 2.2 atoms, max. radius 0.104 nm
Minimum cell size due to atom displacement: 0.596 nm
Initial maximum distances in bonded interactions:
two-body bonded interactions: 0.393 nm, LJ-14, atoms 9 19
multi-body bonded interactions: 0.393 nm, Proper Dih., atoms 9 19
Minimum cell size due to bonded interactions: 0.432 nm
Using 0 separate PME ranks because: there are too few total ranks for efficient splitting
Optimizing the DD grid for 1 cells with a minimum initial size of 0.596 nm
The maximum allowed number of cells is: X 3 Y 3 Z 3
Domain decomposition grid 1 x 1 x 1, separate PME ranks 0
PME domain decomposition: 1 x 1 x 1
The initial number of communication pulses is:
The initial domain decomposition cell size is:
The maximum allowed distance for atom groups involved in interactions is:
non-bonded interactions 1.008 nm
two-body bonded interactions (-rdd) 1.008 nm
multi-body bonded interactions (-rdd) 1.008 nm
When dynamic load balancing gets turned on, these settings will change to:
The maximum number of communication pulses is:
The minimum size for domain decomposition cells is 1.008 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is:
The maximum allowed distance for atom groups involved in interactions is:
non-bonded interactions 1.008 nm
two-body bonded interactions (-rdd) 1.008 nm
multi-body bonded interactions (-rdd) 1.008 nm
NOTE: GROMACS was compiled without OpenMP and (thread-)MPI support, can only use a single CPU core
Pinning threads with an auto-selected logical core stride of 2
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 0.231287 nm for Ewald
Potential shift: LJ r^-12: -1.455e+01 r^-6: -3.815e+00, Ewald -1.250e-06
Initialized non-bonded Ewald tables, spacing: 7.93e-04 size: 1010
Generated table with 3600 data points for 1-4 COUL.
Tabscale = 2000 points/nm
Generated table with 3600 data points for 1-4 LJ6.
Tabscale = 2000 points/nm
Generated table with 3600 data points for 1-4 LJ12.
Tabscale = 2000 points/nm
Long Range LJ corr.: <C6> 5.4181e-04
Using plain C 4x4 nonbonded short-range kernels
WARNING: Using the slow plain C kernels. This should
not happen during routine usage on supported platforms.
Using a 4x4 pair-list setup:
updated every 100 steps, buffer 0.000 nm, rlist 0.800 nm
At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
updated every 100 steps, buffer 0.000 nm, rlist 0.800 nm
Using Lorentz-Berthelot Lennard-Jones combination rule
Removing pbc first time
Linking all bonded interactions to atoms
Will apply potential COM pulling
with 1 pull coordinate and 3 groups
Pull group 1: 1 atoms, mass 12.010
Pull group 2: 1 atoms, mass 12.010
Pull group 3: 1 atoms, mass 12.010
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 12
++++ 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: 22 Atoms
Atom distribution over 1 domains: av 22 stddev 0 min 22 max 22
Constraining the starting coordinates (step 0)
Constraining the coordinates at t0-dt (step 0)
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: System
RMS relative constraint deviation after constraining: 0.00e+00
Initial temperature: 349.716 K
Started mdrun on rank 0 Tue Nov 23 15:07:17 2021
Step Time
0 0.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
1.27427e+01 2.81264e+01 4.03711e+01 4.13339e+00 1.29447e+01
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
1.94121e+02 -5.93191e+00 -1.06537e-01 -3.60409e+02 2.88119e+01
COM Pull En. Potential Kinetic En. Total Energy Conserved En.
6.98720e-07 -4.51961e+01 7.62028e+01 3.10067e+01 3.10067e+01
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
3.59415e+02 -1.29344e-01 8.15882e+01 0.00000e+00
Step Time
20 0.04000
Writing checkpoint, step 20 at Tue Nov 23 15:07:17 2021
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
1.09068e+01 4.01865e+01 4.54116e+01 2.06231e+00 1.32480e+01
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
2.06835e+02 -6.79589e+00 -1.06537e-01 -3.69157e+02 2.85535e+01
COM Pull En. Potential Kinetic En. Total Energy Conserved En.
2.40361e-01 -2.86144e+01 6.07571e+01 3.21428e+01 3.14106e+01
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
2.86565e+02 -1.29344e-01 2.38456e+02 0.00000e+00
Energy conservation over simulation part #1 of length 0.04 ns, time 0 to 0.04 ns
Conserved energy drift: 4.59e-01 kJ/mol/ps per atom
<====== ############### ==>
<==== A V E R A G E S ====>
<== ############### ======>
Statistics over 21 steps using 21 frames
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
8.37574e+00 3.47895e+01 4.42483e+01 2.69036e+00 1.58232e+01
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
2.03807e+02 -6.89228e+00 -1.06537e-01 -3.64751e+02 2.90456e+01
COM Pull En. Potential Kinetic En. Total Energy Conserved En.
6.42806e-01 -3.23275e+01 6.55701e+01 3.32426e+01 3.16107e+01
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
3.09266e+02 -1.29344e-01 9.34857e+01 0.00000e+00
Total Virial (kJ/mol)
-2.97383e+01 7.19789e+00 8.07512e+00
7.19789e+00 -7.26246e+01 -1.59127e-01
8.07512e+00 -1.59127e-01 2.77822e+01
Pressure (bar)
1.17313e+02 -9.09186e+00 -1.16631e+01
-9.09186e+00 1.80343e+02 -5.15862e+00
-1.16631e+01 -5.15862e+00 -1.71988e+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
-----------------------------------------------------------------------------
Pair Search distance check 0.000608 0.005 0.0
NxN QSTab Elec. + LJ [V&F] 0.008736 0.515 0.8
NxN QSTab Elec. [V&F] 0.000672 0.028 0.0
1,4 nonbonded interactions 0.000861 0.077 0.1
Calc Weights 0.001386 0.050 0.1
Spread Q Bspline 0.029568 0.059 0.1
Gather F Bspline 0.029568 0.177 0.3
3D-FFT 7.986174 63.889 96.8
Solve PME 0.012096 0.774 1.2
Reset In Box 0.000022 0.000 0.0
CG-CoM 0.000044 0.000 0.0
Bonds 0.000189 0.011 0.0
Angles 0.000756 0.127 0.2
Propers 0.000798 0.183 0.3
Impropers 0.000084 0.017 0.0
Virial 0.001407 0.025 0.0
Stop-CM 0.000088 0.001 0.0
Calc-Ekin 0.000484 0.013 0.0
Lincs 0.000276 0.017 0.0
Lincs-Mat 0.002484 0.010 0.0
Constraint-V 0.000528 0.005 0.0
Constraint-Vir 0.000252 0.006 0.0
-----------------------------------------------------------------------------
Total 65.991 100.0
-----------------------------------------------------------------------------
D O M A I N D E C O M P O S I T I O N S T A T I S T I C S
av. #atoms communicated per step for force: 2 x 0.0
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 %
-----------------------------------------------------------------------------
Domain decomp. 1 1 1 0.000 0.001 0.3
Neighbor search 1 1 1 0.000 0.001 0.3
Force 1 1 21 0.002 0.006 3.4
PME mesh 1 1 21 0.057 0.147 77.9
NB X/F buffer ops. 1 1 41 0.000 0.000 0.1
COM pull force 1 1 21 0.000 0.001 0.3
Write traj. 1 1 21 0.010 0.025 13.5
Update 1 1 21 0.000 0.001 0.4
Constraints 1 1 23 0.001 0.002 1.2
Rest 0.002 0.005 2.6
-----------------------------------------------------------------------------
Total 0.073 0.188 100.0
-----------------------------------------------------------------------------
Breakdown of PME mesh computation
-----------------------------------------------------------------------------
PME spread 1 1 21 0.003 0.007 3.8
PME gather 1 1 21 0.001 0.004 1.9
PME 3D-FFT 1 1 42 0.032 0.082 43.8
PME solve Elec 1 1 21 0.021 0.053 28.3
-----------------------------------------------------------------------------
Core t (s) Wall t (s) (%)
Time: 0.072 0.073 99.5
(ns/day) (hour/ns)
Performance: 49.952 0.480
Finished mdrun on rank 0 Tue Nov 23 15:07:17 2021
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