[gmx-users] trajectory file

Smith, Micholas D. smithmd at ornl.gov
Fri Dec 4 14:04:57 CET 2015

Although you should ask these type of questions to the VMD mailing list, since the trjaectory file format is typical of md simulations from gromacs, I'll give you a quick answer:

VMD needs to know the atom names/types in order to draw anything, these are not stored in the xtc file. Instead you need to load your geometry into vmd first (your .gro or .pdb file) for your system, and then load the trajectory as data into the "molecule" that vmd generates on screen. Alternatively, you can use gmx trjconv to convert your trajectory file from xtc to pdb (or gro) and read the multi-frame pdb or gro file into vmd (these files will have multiple frames, and the atom names, but can be fairly large in terms of disk space).

Also, welcome to the wonderful world of MD simulations!

Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: Friday, December 04, 2015 7:29 AM
To: gmx-users at gromacs.org; mihammad roos
Subject: Re: [gmx-users] trajectory file

On 12/3/15 4:39 PM, mihammad roos wrote:
> Hi everybody,
> I ran the production MD and got the trajectory file (xtcformat) but as I’m new to MD I don’t know how to visualize it. I opened it withvmd and it could read the atoms and frames but didn’t show anything when playingthe frames. I don’t know whether another program can do it or my xtc is notcorrect.

Try some VMD tutorials. Loading coordinates and subsequently trajectories (as
data for those initial coordinates) is covered in any basic tutorial. Ask VMD
questions on the VMD mailing list.



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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