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

[David van der Spoel]

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