[gmx-users] Different system volumes from gromacs versions 3.2.1 and 3.3.1

sapna sarupria sapna.sarupria at gmail.com
Tue Dec 18 17:10:32 CET 2007


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" <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
> Message-ID:
>        <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>
> 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>
> Message-ID: <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    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
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