[gmx-users] how to adjust the box size to correct density?
Chang Woon Jang
changwoonjang at gmail.com
Tue Jan 5 21:39:17 CET 2016
Dear Mark,
I obtained the tpr file with gro and topology file using grompp -v.
The following is from md.log file.
Best regards,
Changwoon Jang
Log file opened on Fri Nov 13 13:52:29 2015
Host: c438-702.stampede.tacc.utexas.edu pid: 8923 rank ID: 0 number of
ranks: 64
GROMACS: mdrun_mpi, VERSION 5.0.6
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
Gerrit Groenhof Christoph Junghans Peter Kasson Carsten Kutzner
Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
Peter Tieleman 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) 2001-2014, 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: mdrun_mpi, VERSION 5.0.6
Executable:
/opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/bin/mdrun_mpi
Library dir:
/opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/share/gromacs/top
Command line:
mdrun_mpi -v
Gromacs version: VERSION 5.0.6
Precision: single
Memory model: 64 bit
MPI library: MPI
OpenMP support: enabled
GPU support: disabled
invsqrt routine: gmx_software_invsqrt(x)
SIMD instructions: AVX_256
FFT library: Intel MKL
RDTSCP usage: enabled
C++11 compilation: enabled
TNG support: enabled
Tracing support: disabled
Built on: Wed Sep 9 15:35:09 CDT 2015
Built by: micbuild at c560-901.stampede.tacc.utexas.edu [CMAKE]
Build OS/arch: Linux 2.6.32-431.17.1.el6.x86_64 x86_64
Build CPU vendor: GenuineIntel
Build CPU brand: Intel(R) Xeon(R) CPU E5-2680 0 @ 2.70GHz
Build CPU family: 6 Model: 45 Stepping: 7
Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr
nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1
sse4.2 ssse3 tdt x2apic
C compiler:
/opt/apps/intel/15/composer_xe_2015.2.164/bin/intel64/icc Intel
15.0.2.20150121
C compiler flags: -mavx -mkl=sequential -O3 -funroll-all-loops
-std=gnu99 -w3 -wd111 -wd177 -wd181 -wd193 -wd271 -wd304 -wd383 -wd424
-wd444 -wd522 -wd593 -wd869 -wd981 -wd1418 -wd1419 -wd1572 -wd1599 -wd2259
-wd2415 -wd2547 -wd2557 -wd3280 -wd3346 -wd11074 -wd11076 -O3 -DNDEBUG -ip
-funroll-all-loops -alias-const -ansi-alias
C++ compiler:
/opt/apps/intel/15/composer_xe_2015.2.164/bin/intel64/icpc Intel
15.0.2.20150121
C++ compiler flags: -mavx -std=c++0x -O3 -funroll-all-loops -w3 -wd111
-wd177 -wd181 -wd193 -wd271 -wd304 -wd383 -wd424 -wd444 -wd522 -wd593
-wd869 -wd981 -wd1418 -wd1419 -wd1572 -wd1599 -wd2259 -wd2415 -wd2547
-wd2557 -wd3280 -wd3346 -wd11074 -wd11076 -wd1782 -wd2282 -O3 -DNDEBUG -ip
-funroll-all-loops -alias-const -ansi-alias
Boost version: 1.55.0 (external)
Number of hardware threads detected (16) does not match the number reported
by OpenMP (1).
Consider setting the launch configuration manually!
Changing nstlist from 5 to 40, rlist from 1.22 to 1.22
Input Parameters:
integrator = md
tinit = 0
dt = 0.001
nsteps = 10000000
init-step = 0
simulation-part = 1
comm-mode = Linear
nstcomm = 50
bd-fric = 0
ld-seed = 1993
emtol = 100
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
rtpi = 0.05
nstxout = 1000
nstvout = 0
nstfout = 1000
nstlog = 50
nstcalcenergy = 50
nstenergy = 50
nstxout-compressed = 0
compressed-x-precision = 1000
cutoff-scheme = Verlet
nstlist = 40
ns-type = Grid
pbc = xyz
periodic-molecules = FALSE
verlet-buffer-tolerance = 0.005
rlist = 1.22
rlistlong = 1.22
nstcalclr = 5
coulombtype = PME
coulomb-modifier = Potential-shift
rcoulomb-switch = 0
rcoulomb = 1.22
epsilon-r = 1
epsilon-rf = inf
vdw-type = Cut-off
vdw-modifier = Potential-shift
rvdw-switch = 0
rvdw = 1.22
DispCorr = EnerPres
table-extension = 1
fourierspacing = 0.12
fourier-nx = 84
fourier-ny = 84
fourier-nz = 84
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 = 2
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 = Nose-Hoover
nsttcouple = 5
nh-chain-length = 1
print-nose-hoover-chain-variables = FALSE
pcoupl = No
pcoupltype = Isotropic
nstpcouple = -1
tau-p = 0.5
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
....
On Tue, Jan 5, 2016 at 3:07 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> Hi,
>
> On Tue, Jan 5, 2016 at 7:15 PM Chang Woon Jang <changwoonjang at gmail.com>
> wrote:
>
> > Dear Gromacs Users,
> >
> >
> > I have a low density polymer system initially. I would like to fit the
> > correct liquid density using NPT simulation.
> >
> > I used Pcoupl=berendsen for 22 ns but the box size in confout.gro is
> still
> > the same as the input size of conf.gro.
> >
> > Initial in conf.gro (10.0 10.0 9.8)
> > output in confout.gro (10.0 10.0 9.8)
> >
>
> That's wildly unlikely if you've used the .tpr with the contents that you
> think you have. Inspect the top of your .log file to see.
>
> Mark
>
>
> > My initial conditions are
> >
> > tau_p=5.0
> > compressibility=4.5e-5
> > ref_p=1.0
> >
> > Do I need to increase compressibility?
> >
> > Thank you.
> >
> > Best regards,
> > Changwoon Jang,
> > --
> > Gromacs Users mailing list
> >
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--
Best regards,
Changwoon Jang,
Postdoctoral Research Fellow
Department of Chemical & Biological Engineering, Drexel University
3141 Chestnut Street, Philadelphia, PA 19104
Voice: (662) 617-2267
E-mail: cj395 at drexel.edu
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