[gmx-users] About free energy Methods for Memebrane-protein Calculation
jalemkul at vt.edu
Wed Dec 18 18:40:50 CET 2013
On 12/18/13 9:57 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. Normally Membrane Tutorail Does not contain Free Energy Calculation.
> So which Method is Suitable to study this kind of free energy
Probably umbrella sampling.
> Is ther is Any suitable Tutorial ?
> Also Parallely I am running on Namd
> I would Loke to Convert .dcd files of Namd to either .Tpr or .Trr files of Gromacs for Analysis purpose
> Is thers is Any Script,or Server or tools Available for this?
catdcd can convert between formats. You will have to correct the time steps
using trjconv, or the VMD plugins can be used to read non-Gromacs formats (if
you have installed Gromacs with this capability - see install instructions).
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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