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? 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.