[gmx-users] extracting from TRR

[Justin Lemkul]

On 9/26/14 6:42 AM, N. S. wrote:
> Dear GMX experts,
>
> How could I extract the only state from MD-simulation .TRR (or traj.xtc)
> file that has the lowest RMSD from the reference protein.pdb file?
> Please give me a line of code in UBUNTU or the script.

Calculate the RMSD using g_rms, find the minimum value, then extract that frame 
with trjconv -dump.

-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 601
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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