[gmx-users] Different system volumes from gromacs versions 3.2.1 and 3.3.1
David van der Spoel
spoel at xray.bmc.uu.se
Tue Dec 18 19:38:57 CET 2007
sapna sarupria wrote:
> 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.
>
Please submit a bugzilla. The off-diagonal terms in the virial should be
small, which points to a possible error in 3.2.1 rather than 3.3.1. Have
you compared the density with literature values?
> 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" < sapna.sarupria at gmail.com
> <mailto:sapna.sarupria at gmail.com>>
> Subject: [gmx-users] Different system volumes from gromacs versions
> 3.2.1 and 3.3.1
> To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> Message-ID:
> <3e794d50712180528p1500aefdpb080cbcacf1e537d at mail.gmail.com
> <mailto:3e794d50712180528p1500aefdpb080cbcacf1e537d at mail.gmail.com>>
> 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
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> ------------------------------
>
> Message: 7
> Date: Tue, 18 Dec 2007 15:13:16 +0100
> From: David van der Spoel < spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se>>
> 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 at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <4767D57C.30005 at xray.bmc.uu.se
> <mailto:4767D57C.30005 at xray.bmc.uu.se>>
> 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
> >
> >
> >
> ------------------------------------------------------------------------
>
> >
> > _______________________________________________
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>
>
> --
> 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.
> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
> spoel at gromacs.org <mailto:spoel at gromacs.org> 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 at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
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--
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.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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