[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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