<div class="gmail_quote"><br>Dear users,<br><br> 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. <br><br> 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?
<br><br>Thank you<br><br><br>Regards<br>Sapna<br clear="all"><br>-- <br>Sapna Sarupria<br>Ph.D. Student - Chemical Engineering<br>Rensselaer Polytechnic Institute<br>Troy, New York 12180<br>U.S.A.<br>Ph#: (518)276-3031<br>
Life isn't about finding yourself. Life is about creating yourself. <br>George Bernard Shaw. <br>Dare to Dream
</div><br><br clear="all"><br>-- <br>Sapna Sarupria<br>Ph.D. Student - Chemical Engineering<br>Rensselaer Polytechnic Institute<br>Troy, New York 12180<br>U.S.A.<br>Ph#: (518)276-3031<br>Life isn't about finding yourself. Life is about creating yourself.
<br>George Bernard Shaw. <br>Dare to Dream