[gmx-users] extracting coordinates from traj.xtc

[Justin Lemkul]

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 
file, etc.

-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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