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

sapna sarupria sapna.sarupria at gmail.com
Thu Dec 13 21:38:22 CET 2007

Dear users,

   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
(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 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


Sapna Sarupria
Ph.D. Student - Chemical Engineering
Rensselaer Polytechnic Institute
Troy, New York 12180
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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