[gmx-users] mdp file of membrane simulation

[Justin Lemkul]

On 10/20/16 11:47 AM, Mijiddorj Batsaikhan wrote:
> Thank you very much.
>
> *(1)*
> Which one is suitable the following 2 examples for energy groups in my mdp
> file?
>
> *Example 1*
>
> energygrps = Protein Membrane
> energy grps = r_1 Membrane
> energygrps = r_2 Membrane
> ...
> energygrps = r_N Membrane
>
> *Example 2*
> energygrps = Protein Membrane r_1 r_2 ... r_N
>

This is correct.  As with any .mdp keyword, it can only appear once.

>
> *(2)* -mdrerun is how faster than original md simulation?
>

In general, it takes a few minutes.  Don't waste time with energygrps for the 
original run (if there are many, your run can slow down a lot!) and just treat 
the pairwise energy decomposition as simply analysis.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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