[gmx-users] extracting coordinates from traj.xtc
jalemkul at vt.edu
Wed Dec 2 13:34:12 CET 2015
On 12/1/15 8:21 AM, mah maz wrote:
> Thank you Justin. I expected that only water molecules are written in .xtc
> but all the others are there! g_traj -f traj.xtc -ox gives numbers like
> 1.64e-318 for all frames! How can I get real coordinates from .xtc?
If you've got unexpected content, you need to go back and check everything you
did. Load the trajectory in VMD and watch it; if the geometries go haywire,
then your run probably crashed (as the infinitely small coordinate suggests).
See what gmxcheck has to say, try trjconv -dump to write out a single coordinate
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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