[gmx-users] Justin umbrella sampling tutorial......

Justin A. Lemkul jalemkul at vt.edu
Thu May 24 23:06:06 CEST 2012

On 5/24/12 6:35 AM, rama david wrote:
> Thank you Justin for these correct explanation
> Its really clear my lot of queries..
>     For the tutorial, NPT is conducted with restraints on all protein heavy
>     atoms.  The production runs are conducted by restraining only one chain for
>     practical reasons.
>     These is my question ;
> If we are doing NPT with restraints on all protein atom and production run by
> conducted by restraining only one chain for protein...
> means NPT and productin run mdp files should be different , Where these
> information in mdp files???
> It my request to you please tell me why these mdp files are almost same in
> parameter ..
> (Where you mentioned in mdp for npt to do restraints on all proteins heavy atoms
> and for production md restraining only
> one chain ..)

I don't understand what more I can say beyond what I already have.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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