Query Regarding FEP tutorial: NPT or NVT?

From: mon_sharma_at_research.iiit.ac.in
Date: Sat Oct 11 2008 - 16:33:04 CDT

Hi All,

I was trying the latest FEP tutorial available at NAMD site. I am stuck at
one trivial question regarding alchemical FEP calculation of Ala-Tyr-Ala
to (Ala)3 mutation. The calculations are done in vacuum and in hydrated
state to get del(delG). Its fine. Now when I read through the "Running the
MD simulation" part. For vaccum, as far as I could understand from the
tutorial, it is
NVT simulation and for hydration its NPT one. and the values that comes
after FEP calculations are written as del G (Gibbs free energy). Now the
thing that is bothering me is that NVT corresponds to A (Helmholtz
free energy) and NPT to G (Gibbs free energy). So what are we actually
calculating here, since vacuum is NVT and hydrated state is NPT.
It may be a trivial one, and I might not have been able to understand
fully or may be I am missing something important here. Does NVT calc of
vacuum is equivalent to NPT??

Thanks in advance,


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