[gmx-users] extracting coordinates from traj.xtc

Justin Lemkul jalemkul at vt.edu
Sun Dec 6 15:06:56 CET 2015

On 12/6/15 2:49 AM, mah maz wrote:
> Thank you. I tested gmxdump and also trjconv -dump and compared traj.trr
> and traj.xtc. You are right both have the same data. I just need the
> coordinates to be readable a printable in a file now. Although I can write
> a program to extract the coordinates from gmxdump the way I need, it seems
> a bit time consuming. And I couldn't find a way yet! Is there a command
> like g_traj -f traj.trr -ox to print coordinates from traj.xtc?

Frankly, from the information you're providing (which is vague at best) there is 
nothing I can tell you that will be any use.  The coordinates in .trr and .xtc 
cannot be different (outside of the fact that they are different precision).  It 
is not logical that one file differs from the other unless one of them is 
somehow corrupt.  If the trajectories load fine (e.g. in VMD), gmxcheck reports 
no problems, and coordinate files dumped out of them agree, there is no 
explanation for why you think you have junk coordinates coming out of g_traj. 
You've reported a single number that seems to be wrong but no other context, so 
it's impossible to diagnose this further.


> Thanks!
> On Thu, Dec 3, 2015 at 8:27 PM, mah maz <mahmaz71 at gmail.com> 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?
>> 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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