[gmx-users] extracting coordinates from traj.xtc

Justin Lemkul jalemkul at vt.edu
Fri Dec 4 13:31:28 CET 2015

On 12/3/15 11:57 AM, mah maz wrote:
> Thanks Justin! I checked the run and it seemed ok. The fact is, the data I
> get by g_traj -f traj.trr -ox is reasonable (although I didnt set nstxout
> it was set every 100 step by default), while the same command with g_traj
> -f traj.xtc -ox gives wrong coordinates. Since I need coordinates for every
> step I need to extract them from traj.xtc. Can you suggest any ways?

None of this really makes any sense to me.  The coordinates in the .trr and .xtc 
aren't different, aside from precision.  So it strikes me as wildly unlikely 
that the contents of one are different from the other, unless one file is 
corrupt.  In any case, verifying the contents of the .trr is irrelevant.  Did 
you try what I suggested with trjconv?  Try dumping just the first frame of the 
.xtc and look at it.  Any nonsense coordinates should be blatantly obvious.


> Thank you!
> On Tue, Dec 1, 2015 at 4:51 PM, mah maz <mahmaz71 at gmail.com> 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?
>> Thanks!
>> On Tue, Dec 1, 2015 at 10:34 AM, mah maz <mahmaz71 at gmail.com> wrote:
>>> Dear all,
>>> I have some problems extracting data from traj.xtc. The command " g_traj
>>> -s -ox" doesn't give reasonable coordinates. I tried "trjconv" but again
>>> couldn't get any results.  Note that I have nstxtcout = 1 and xtc_grps =
>>> water in my .mdp file.
>>> Any help is appreciated.
>>> Thank you!


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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