[gmx-users] About free energy Methods for Memebrane-protein Calculation

[Justin Lemkul]

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 ?

Yes.

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html

> 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

-- 
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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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