[gmx-users] Reg Free enerfy calculation

Justin Lemkul 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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