[gmx-users] Reg Free enerfy calculation
jalemkul at vt.edu
Sat May 31 21:15:13 CEST 2014
On 5/31/14, 9:25 AM, vidhya sankar wrote:
> Hi justin ,
> Thank you for your earlier kindful replies
> I need to calcullate Free energy based on your Methane/water (Tutorial5) fo My System ( My system in CNTWrapped by assembly of Cyclic peptide in water as solvent)
> I want to decouple CNT Wrapped by assembly of Cyclic peptide from rest of surrounding solvent (the stability of assembly is mainly due to Vandewall's interaction between CNT and cyclic peptide)
> How to Fix Suitable parameter for My system in mdp files
> sc-alpha ?
> sc-power ?
> sc-sigma ?
Same as the tutorial.
> couple-moltype = SOL( it is okay)
No, that decouples water while leaving the CNT and peptide intact. You said
your goal is to decouple the CNT, so that's what you specify here.
> couple-lambda0 ?
Hard to say. I've never tried to decouple something as large as a CNT, but in
general convergence is a trade-off between window spacing and simulation length.
You may have to try a few combinations to find the one that works best.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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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