[gmx-users] how to adjust the box size to correct density?
Mark Abraham
mark.j.abraham at gmail.com
Tue Jan 5 21:41:22 CET 2016
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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>
>
>
> --
> 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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