[gmx-users] how to adjust the box size to correct density?
Chang Woon Jang
changwoonjang at gmail.com
Tue Jan 5 21:48:53 CET 2016
Dear Mark,
I see. pcoupl = No is obvious. That means when I create tpr file from
grompp.mdp, the pcoupl setting was No instead of berendsen.
Thank you very much.
Best regards,
Changwoon Jang
On Tue, Jan 5, 2016 at 3:41 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> Hi,
>
> Look at what md.log says about the value for pcoupl it read from your .tpr.
> :-)
>
> Mark
>
> On Tue, Jan 5, 2016 at 9:39 PM Chang Woon Jang <changwoonjang at gmail.com>
> wrote:
>
> > 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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> > > >
> > > --
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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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