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" < [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>
Subject: [gmx-users] Different system volumes from gromacs versions
3.2.1 and 3.3.1
To: [email protected] <mailto:[email protected]>
Message-ID:
<[EMAIL PROTECTED]
<mailto:[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]
<mailto:[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 < [email protected]
<mailto:[email protected]>>
Message-ID: <[EMAIL PROTECTED]
<mailto:[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 [email protected]
<mailto:[email protected]>
> 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]
<mailto:[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] <mailto:[EMAIL PROTECTED]>
[EMAIL PROTECTED] <mailto:[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 [email protected]
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
_______________________________________________
gmx-users mailing list [email protected]
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
