[gmx-users] How to save trajectories of our interest into vmd

Justin Lemkul jalemkul at vt.edu
Mon Oct 27 13:06:56 CET 2014

On 10/27/14 1:25 AM, Seera Suryanarayana wrote:
> Dear Gromacs Users
> I would like to analyze frame number 150 to 160 out of 1000 frames. I have
> been trying to load frames of my interest into vmd. But I was not able to
> do it. Please tell me how to use it.

If you're having problems with VMD, they have a mailing list that might suit 
your question better.  If the question relates to how one views or analyzes only 
a subset of a trajectory, it's rather simple.  Gromacs tools make use of the -b 
and -e options, to allow you to -b(egin) and -e(nd) your analysis at any time 
frame in the trajectory.  If you want to visualize only a short segment of the 
trajectory, use trjconv -b and -e (using time in ps, not frame number) to write 
out a new trajectory for visualization.



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


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