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.abra...@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 <changwoonj...@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: micbu...@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.abra...@gmail.com> > > wrote: > > > > > Hi, > > > > > > On Tue, Jan 5, 2016 at 7:15 PM Chang Woon Jang < > changwoonj...@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 > > > > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > > > > > -- > > 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: cj...@drexel.edu > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? 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