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mdp and log files for free energy simulation in Gromacs
Raw
md.log
Log file opened on Thu Jul 18 09:57:46 2019
Host: villin pid: 32726 rank ID: 0 number of ranks: 1
:-) GROMACS - gmx mdrun, 2018.2 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra
Gerrit Groenhof Aleksei Iupinov Christoph Junghans Anca Hamuraru
Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus
Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl
Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola
Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov
Michael Shirts Alfons Sijbers Peter Tieleman 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) 2001-2017, 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 2018.2
Executable: /usr/local/gromacs/2018.2/bin/gmx
Data prefix: /usr/local/gromacs/2018.2
Command line:
gmx mdrun -v -s data/***_ff03-star_tip3p_hremd_rep0.tpr -deffnm data/***_ff03-star_tip3p_hremd_rep0 -nsteps 5000
GROMACS version: 2018.2
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-avx2-avx2_128-avx512
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: disabled
Tracing support: disabled
Built on: 2018-10-04 12:14:38
Built by: daviddesancho@villin [CMAKE]
Build OS/arch: Linux 4.4.0-36-generic x86_64
Build CPU vendor: Intel
Build CPU brand: Intel(R) Core(TM) i7-7700 CPU @ 3.60GHz
Build CPU family: 6 Model: 158 Stepping: 9
Build CPU features: aes apic avx avx2 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
C compiler: /usr/bin/cc GNU 5.4.0
C compiler flags: -march=core-avx2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
C++ compiler: /usr/bin/c++ GNU 5.4.0
C++ compiler flags: -march=core-avx2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
Running on 1 node with total 4 cores, 8 logical cores
Hardware detected:
CPU info:
Vendor: Intel
Brand: Intel(R) Core(TM) i7-7700 CPU @ 3.60GHz
Family: 6 Model: 158 Stepping: 9
Features: aes apic avx avx2 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
Hardware topology: Basic
Sockets, cores, and logical processors:
Socket 0: [ 0 4] [ 1 5] [ 2 6] [ 3 7]
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
Lindahl
GROMACS: High performance molecular simulations through multi-level
parallelism from laptops to supercomputers
SoftwareX 1 (2015) pp. 19-25
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
GROMACS
In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
GROMACS 4.5: a high-throughput and highly parallel open source molecular
simulation toolkit
Bioinformatics 29 (2013) pp. 845-54
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
-------- -------- --- Thank You --- -------- --------
Input Parameters:
integrator = sd
tinit = 0
dt = 0.002
nsteps = 5000000
init-step = 0
simulation-part = 1
comm-mode = Linear
nstcomm = 100
bd-fric = 0
ld-seed = -170014068
emtol = 10
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
rtpi = 0.05
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstcalcenergy = 100
nstenergy = 1000
nstxout-compressed = 1000
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 = No
table-extension = 1
fourierspacing = 0.12
fourier-nx = 25
fourier-ny = 25
fourier-nz = 25
pme-order = 4
ewald-rtol = 1e-05
ewald-rtol-lj = 0.001
lj-pme-comb-rule = Geometric
ewald-geometry = 0
epsilon-surface = 0
implicit-solvent = No
gb-algorithm = Still
nstgbradii = 1
rgbradii = 1
gb-epsilon-solvent = 80
gb-saltconc = 0
gb-obc-alpha = 1
gb-obc-beta = 0.8
gb-obc-gamma = 4.85
gb-dielectric-offset = 0.009
sa-algorithm = Ace-approximation
sa-surface-tension = 2.05016
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 = yes
init-lambda = -1
init-lambda-state = 0
delta-lambda = 0
nstdhdl = 0
n-lambdas = 12
separate-dvdl:
fep-lambdas = FALSE
mass-lambdas = FALSE
coul-lambdas = FALSE
vdw-lambdas = TRUE
bonded-lambdas = FALSE
restraint-lambdas = FALSE
temperature-lambdas = FALSE
all-lambdas:
fep-lambdas = 0 0 0 0 0 0 0 0 0 0 0 0
mass-lambdas = 0 0 0 0 0 0 0 0 0 0 0 0
coul-lambdas = 0 0 0 0 0 0 0 0 0 0 0 0
vdw-lambdas = 0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
bonded-lambdas = 0 0 0 0 0 0 0 0 0 0 0 0
restraint-lambdas = 0 0 0 0 0 0 0 0 0 0 0 0
temperature-lambdas = 0 0 0 0 0 0 0 0 0 0 0 0
calc-lambda-neighbors = 1
dhdl-print-energy = no
sc-alpha = 0
sc-power = 1
sc-r-power = 6
sc-sigma = 0.3
sc-sigma-min = 0.3
sc-coul = false
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
grpopts:
nrdf: 433.757 4911.24
ref-t: 300 300
tau-t: 1 1
annealing: No No
annealing-npoints: 0 0
acc: 0 0 0
nfreeze: N N N
energygrp-flags[ 0]: 0
The -nsteps functionality is deprecated, and may be removed in a future version. Consider using gmx convert-tpr -nsteps or changing the appropriate .mdp file field.
Overriding nsteps with value passed on the command line: 5000 steps, 10 ps
Changing nstlist from 10 to 50, rlist from 1 to 1.106
Using 1 MPI thread
Using 8 OpenMP threads
Pinning threads with an auto-selected logical core stride of 1
System total charge, top. A: -0.000 top. B: -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
Generated table with 1053 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1053 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1053 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 0.106 nm, rlist 1.106 nm
inner list: updated every 12 steps, buffer 0.001 nm, rlist 1.001 nm
At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
outer list: updated every 50 steps, buffer 0.232 nm, rlist 1.232 nm
inner list: updated every 12 steps, buffer 0.046 nm, rlist 1.046 nm
Using full Lennard-Jones parameter combination matrix
There are 1 atoms and 0 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 76
++++ 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 --- -------- --------
Intra-simulation communication will occur every 50 steps.
Initial vector of lambda components:[ 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 ]
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 ++++
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: 2627 Atoms
Started mdrun on rank 0 Thu Jul 18 09:57:46 2019
Step Time
0 0.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
2.01353e+02 4.00667e+02 3.88943e+02 3.36948e+01 1.12376e+02
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
2.13766e+03 4.78357e+03 -3.90804e+04 2.49415e+02 -3.07727e+04
Kinetic En. Total Energy Temperature Pressure (bar) dVvdw/dl
6.79380e+03 -2.39789e+04 3.05746e+02 3.30325e+01 1.19776e+02
Constr. rmsd
2.28792e-06
Step Time
1000 2.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
2.47040e+02 4.38924e+02 3.80580e+02 2.02703e+01 1.05956e+02
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
2.07509e+03 5.08194e+03 -3.95281e+04 2.73239e+02 -3.09051e+04
Kinetic En. Total Energy Temperature Pressure (bar) dVvdw/dl
6.93667e+03 -2.39684e+04 3.12176e+02 -1.53521e+02 1.05187e+02
Constr. rmsd
1.77294e-06
Step Time
2000 4.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
3.10763e+02 4.23020e+02 3.98769e+02 1.82230e+01 1.04596e+02
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
2.06925e+03 5.12194e+03 -3.97175e+04 2.64857e+02 -3.10061e+04
Kinetic En. Total Energy Temperature Pressure (bar) dVvdw/dl
6.59510e+03 -2.44110e+04 2.96804e+02 -5.70691e+02 1.28614e+02
Constr. rmsd
1.96026e-06
Step Time
3000 6.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
2.76652e+02 4.01297e+02 3.51716e+02 2.86213e+01 1.03946e+02
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
2.09836e+03 5.04498e+03 -3.94263e+04 2.48457e+02 -3.08723e+04
Kinetic En. Total Energy Temperature Pressure (bar) dVvdw/dl
6.49986e+03 -2.43724e+04 2.92518e+02 -3.77829e+02 1.47757e+02
Constr. rmsd
1.13723e-06
Step Time
4000 8.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
2.63492e+02 4.33936e+02 3.71144e+02 2.59051e+01 1.23445e+02
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
2.06444e+03 4.91638e+03 -3.94856e+04 2.45089e+02 -3.10417e+04
Kinetic En. Total Energy Temperature Pressure (bar) dVvdw/dl
6.48491e+03 -2.45568e+04 2.91845e+02 -5.70980e+02 1.07950e+02
Constr. rmsd
2.54877e-06
Step Time
5000 10.00000
Writing checkpoint, step 5000 at Thu Jul 18 09:59:36 2019
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
3.09454e+02 3.95366e+02 4.20552e+02 3.41107e+01 1.06824e+02
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
2.08207e+03 5.43388e+03 -3.99694e+04 2.37790e+02 -3.09494e+04
Kinetic En. Total Energy Temperature Pressure (bar) dVvdw/dl
6.53149e+03 -2.44179e+04 2.93941e+02 1.84860e+02 1.12813e+02
Constr. rmsd
1.58227e-06
<====== ############### ==>
<==== A V E R A G E S ====>
<== ############### ======>
Statistics over 5001 steps using 51 frames
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
2.62154e+02 4.35169e+02 3.90703e+02 2.25130e+01 1.18153e+02
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
2.07348e+03 5.06063e+03 -3.95403e+04 2.57767e+02 -3.09198e+04
Kinetic En. Total Energy Temperature Pressure (bar) dVvdw/dl
6.66322e+03 -2.42566e+04 2.99869e+02 -3.47364e+01 1.30869e+02
Constr. rmsd
0.00000e+00
Total Virial (kJ/mol)
2.25903e+03 -3.79681e+01 -1.26974e+02
-3.79463e+01 2.34092e+03 1.28350e+01
-1.26970e+02 1.28019e+01 2.14726e+03
Pressure (bar)
-4.83333e+01 4.90309e+01 1.62714e+02
4.90038e+01 -1.41140e+02 -9.58144e+00
1.62709e+02 -9.54046e+00 8.52646e+01
T-Protein T-non-Protein
3.00284e+02 2.99833e+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
-----------------------------------------------------------------------------
NB Free energy kernel 571103.650890 571103.651 52.4
Pair Search distance check 104.708894 942.380 0.1
NxN Ewald Elec. + LJ [F] 4083.782768 269529.663 24.7
NxN Ewald Elec. + LJ [V&F] 42.063936 4500.841 0.4
NxN Ewald Elec. [F] 3471.179760 211741.965 19.4
NxN Ewald Elec. [V&F] 35.815968 3008.541 0.3
1,4 nonbonded interactions 2.070414 186.337 0.0
Calc Weights 39.412881 1418.864 0.1
Spread Q Bspline 840.808128 1681.616 0.2
Gather F Bspline 840.808128 5044.849 0.5
3D-FFT 2177.235360 17417.883 1.6
Solve PME 3.125625 200.040 0.0
Shift-X 0.265327 1.592 0.0
Bonds 0.480096 28.326 0.0
Angles 1.460292 245.329 0.0
Propers 2.080416 476.415 0.0
Impropers 0.270054 56.171 0.0
Virial 0.136272 2.453 0.0
Update 13.137627 407.266 0.0
Stop-CM 0.133977 1.340 0.0
Calc-Ekin 0.530654 14.328 0.0
Lincs 0.760152 45.609 0.0
Lincs-Mat 2.160432 8.642 0.0
Constraint-V 26.095218 208.762 0.0
Constraint-Vir 0.129183 3.100 0.0
Settle 8.191638 2645.899 0.2
-----------------------------------------------------------------------------
Total 1090921.862 100.0
-----------------------------------------------------------------------------
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 8 OpenMP threads
Computing: Num Num Call Wall time Giga-Cycles
Ranks Threads Count (s) total sum %
-----------------------------------------------------------------------------
Neighbor search 1 8 101 0.547 15.741 0.5
Force 1 8 5001 104.463 3008.513 94.5
PME mesh 1 8 5001 1.333 38.378 1.2
NB X/F buffer ops. 1 8 9901 3.627 104.456 3.3
Write traj. 1 8 6 0.017 0.482 0.0
Update 1 8 10002 0.256 7.373 0.2
Constraints 1 8 10002 0.196 5.635 0.2
Rest 0.068 1.964 0.1
-----------------------------------------------------------------------------
Total 110.506 3182.542 100.0
-----------------------------------------------------------------------------
Breakdown of PME mesh computation
-----------------------------------------------------------------------------
PME spread 1 8 5001 0.472 13.586 0.4
PME gather 1 8 5001 0.345 9.936 0.3
PME 3D-FFT 1 8 10002 0.427 12.311 0.4
PME solve Elec 1 8 5001 0.039 1.134 0.0
-----------------------------------------------------------------------------
Core t (s) Wall t (s) (%)
Time: 884.045 110.506 800.0
(ns/day) (hour/ns)
Performance: 7.820 3.069
Finished mdrun on rank 0 Thu Jul 18 09:59:36 2019
Raw
sd_free.mdp
integrator = sd
dt = 0.002 ; in ps
nsteps = 5000000
nstlog = 1000
nstenergy = 1000
;energygrps = Protein non-Protein
nstxout-compressed = 1000
compressed-x-grps = non-Water
continuation = yes
constraint_algorithm = lincs
constraints = h-bonds
lincs_iter = 1
lincs_order = 4
nstlist = 10
ns_type = grid
cutoff-scheme = verlet
coulombtype = pme
rvdw = 1.
rcoulomb = 1.
tc_grps = protein non-protein
tau_t = 1 1
ref_t = 300.0 300.0
Pcoupl = no
gen_vel = no
; H-REPLEX
free-energy = yes
init-lambda-state = 0
nstdhdl = 0
vdw_lambdas = 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
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