[gmx-users] Abot Free energy methods in gromacs
jalemkul at vt.edu
Fri Dec 20 18:24:38 CET 2013
On 12/20/13 11:10 AM, vidhya sankar wrote:
> Dear Justin ,
> Thank you for your Previous reply.
> I am Doing Simulation of assembly of Cyclic Petide in POPC membrane
> For that I need to calculate Free energy for Stability of Assembly.
> You suggested the Umbrella sampling
> But Aprt from that i wish to do
> Free energy perturbation method or MM-PBSA method
> Is the Afore said method is suitable or Not . to study of assembly of Cyclic Peptide in POPC membrane
I don't see any reason why you would necessarily approach your simulations using
these methods. FEP is certainly a poor choice. Consult the literature, find
what other people do, and develop a sensible protocol based upon your scrutiny
of those methods, your knowledge of your system, and your own goals in
conducting the simulations.
Justin A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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