[gmx-users] Abot Free energy methods in gromacs

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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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