Hello, Thanks for your response. I have used the same tpr files for both the simulations. I compiled the tpr file in gromacs 3.2.1 and then used that tpr file to run simulations using the two versions of gromacs (i.e. only the mdrun was from different versions). I am not using any dispersion correction. There is also no switch or shift being used. I have pasted the run.mdp file below. The energies are different in the two cases. The LJ(SR) and the Coulomb are both different, resulting in different potential energies (PE) for the two. The PE of gromacs v3.3.1 is higher than that obtained by gromacs v3.2.1 (i.e v3.2.1 is more negative). In the pressure virials, I find that the diagonal terms are the same for the two versions (Vir-XX,YY and ZZ) however the off-diagonal are significantly different (magnitude of v3.2.1 > v3.3.1),given below. Does this information give any indication as to what may be wrong? If not I will submit the tpr file to bugzilla.
Thank you Sapna quantity gromacs v3.2.1 gromacs v3.3.1 Pressure (bar) 0.596018 0.838094 Vir-XX 26640.5 26661.2 Vir-XY 6865.12 1.36518 Vir-XZ 6865.21 0.0121227 Vir-YX 6865.8 1.48257 Vir-YY 26652.3 26642.1 Vir-YZ 6886.45 3.93327 Vir-ZX 6861.23 -0.0529923 Vir-ZY 6882.24 3.87739 Vir-ZZ 26665 26647.2 Run.mdp file: title = Water simulation ; a string cpp = /lib/cpp ; c-preprocessor dt = 0.002 ; time step (ps) nsteps = 1000000 ; number of steps nstcomm = 1 ; reset c.o.m. motion nstxout = 500 ; write coords nstvout = 500 ; write velocities nstlog = 100 ; print to logfile nstenergy = 500 ; print energies nstlist = 10 ; update pairlist ns_type = grid ; pairlist method coulombtype = PME rvdw = 1.0 ; cut-off for vdw rcoulomb = 1.0 ; cut-off for coulomb rlist = 1.0 ; cut-off for coulomb Tcoupl = Berendsen tc-grps = System tau_t = 0.5 ref_t = 300 Pcoupl = Berendsen Pcoupltype = isotropic ; pressure geometry tau_p = 0.5 ; p-coupoling time compressibility = 4.5e-5 ; compressibility ref_p = 1.0 ; reference pressure gen_vel = yes ; generate initial velocities gen_temp = 300 ; initial temperature gen_seed = 2432384243 ; random seed Date: Tue, 18 Dec 2007 08:28:52 -0500 > From: "sapna sarupria" <[EMAIL PROTECTED]> > Subject: [gmx-users] Different system volumes from gromacs versions > 3.2.1 and 3.3.1 > To: gmx-users@gromacs.org > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="iso-8859-1" > > Dear users, > > I had posted this question earlier too but did not get any response. I > am > re-posting it hoping someone can clarify this for me. > > I performed NPT simulations of few different systems using both gromacs > v3.2.1 and v3.3.1. I use exactly the same parameters, starting files, > topology files etc for both the versions. The systems are pure water > system > (spc/e 10684 water molecules) and a protein-water system. However, the > average volume of the system that I get is from the simulations is > different > for the two versions. In case of pure water, gromacs v3.2.1 gives me a > lower > volume (~311.497 nm^3) than v3.3.1 (~324.604 nm^3) and the difference is > significantly higher than the fluctuations in the volume. The pressure is > maintained at 1 bar and the temperature is maintained at 300 K using > Berendsen barostat and thermostat respectively. I used SETTLE to maintain > water geometry. I was wondering if someone could tell me why this happens? > Has there been a modification in the pressure virial calculation or > something related to the same that leads to these differences? > > Thank you > > > Regards > Sapna > > -- > Sapna Sarupria > Ph.D. Student - Chemical Engineering > Rensselaer Polytechnic Institute > Troy, New York 12180 > U.S.A. > Ph#: (518)276-3031 > Life isn't about finding yourself. Life is about creating yourself. > George Bernard Shaw. > Dare to Dream > > > > -- > Sapna Sarupria > Ph.D. Student - Chemical Engineering > Rensselaer Polytechnic Institute > Troy, New York 12180 > U.S.A. > Ph#: (518)276-3031 > Life isn't about finding yourself. Life is about creating yourself. > George Bernard Shaw. > Dare to Dream > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20071218/f2801895/attachment-0001.html > > ------------------------------ > > Message: 7 > Date: Tue, 18 Dec 2007 15:13:16 +0100 > From: David van der Spoel <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Different system volumes from gromacs > versions 3.2.1 and 3.3.1 > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > sapna sarupria wrote: > > > > Dear users, > > > > I had posted this question earlier too but did not get any response. > > I am re-posting it hoping someone can clarify this for me. > > > > I performed NPT simulations of few different systems using both > > gromacs v3.2.1 and v3.3.1. I use exactly the same parameters, starting > > files, topology files etc for both the versions. The systems are pure > > water system (spc/e 10684 water molecules) and a protein-water system. > > However, the average volume of the system that I get is from the > > simulations is different for the two versions. In case of pure water, > > gromacs v3.2.1 gives me a lower volume (~311.497 nm^3) than v3.3.1 > > (~324.604 nm^3) and the difference is significantly higher than the > > fluctuations in the volume. The pressure is maintained at 1 bar and the > > temperature is maintained at 300 K using Berendsen barostat and > > thermostat respectively. I used SETTLE to maintain water geometry. I was > > wondering if someone could tell me why this happens? Has there been a > > modification in the pressure virial calculation or something related to > > the same that leads to these differences? > > > Have you checked the energy differences? > > Have you compared tpr files? > > Is the dispersion correction on and are you using some kind of > shift/switch? (This has changed between 3.2 and 3.3). > > If you can not find the reason for this and it is reproducible then > please submit a bugzilla with a 3.2.1 tpr file that reproduces the > problem. > > Thank you > > > > > > Regards > > Sapna > > > > -- > > Sapna Sarupria > > Ph.D. Student - Chemical Engineering > > Rensselaer Polytechnic Institute > > Troy, New York 12180 > > U.S.A. > > Ph#: (518)276-3031 > > Life isn't about finding yourself. Life is about creating yourself. > > George Bernard Shaw. > > Dare to Dream > > > > > > > > -- > > Sapna Sarupria > > Ph.D. Student - Chemical Engineering > > Rensselaer Polytechnic Institute > > Troy, New York 12180 > > U.S.A. > > Ph#: (518)276-3031 > > Life isn't about finding yourself. Life is about creating yourself. > > George Bernard Shaw. > > Dare to Dream > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > David van der Spoel, Ph.D. > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > > > ------------------------------ > > Sapna Sarupria Ph.D. Student - Chemical Engineering Rensselaer Polytechnic Institute Troy, New York 12180 U.S.A. Ph#: (518)276-3031 Life isn't about finding yourself. Life is about creating yourself. George Bernard Shaw. Dare to Dream
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php