[gmx-users] doubt regarding mdp option for rerun

[Justin Lemkul]

On 10/13/16 9:50 AM, Tushar Ranjan Moharana wrote:
> Hi Everyone,
> I have extended my simulation from 6 ns to 20 ns. Now I want to rerun to
> calculate energy between various energy groups. I have 2 xtc files one
> having first 6ns and one with 14 ns (7th to 20th) (Even though I used
> append during mdrun). My doubts are:
> 1) What will be the mdp option for nsteps, if I want to rerun only the
> second xtc.

Shouldn't matter, but it's simple to calculate.  time / dt = number of steps.

> 2) Can I combine them to get a continuous xtc file.
>

That's what trjcat is for.

-Justin

-- 
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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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