[gmx-users] extracting coordinates from traj.xtc

Justin Lemkul jalemkul at vt.edu
Sun Dec 6 15:07:07 CET 2015

On 12/6/15 2:56 AM, mah maz wrote:
> And also, if I want velocities for every step what can I do?

nstvout = 1


> Thanks!
> On Sun, Dec 6, 2015 at 11:19 AM, mah maz <mahmaz71 at gmail.com> 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?
>> 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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