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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