From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Sat Oct 11 2008 - 18:05:52 CDT
I am fairly certain this is a typo. Helmholtz free energies are obtained
from isothermal ensembles (NVT). Gibbs free energies are obtained from
isothermal, isobaric ensembles (NPT).
On Sat, Oct 11, 2008 at 4:33 PM, <mon_sharma_at_research.iiit.ac.in> wrote:
> 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,
-- Chris Harrison, Ph.D. Theoretical and Computational Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 char_at_ks.uiuc.edu Voice: 217-244-1733 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
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