[gmx-users] extracting coordinates from traj.xtc

mah maz mahmaz71 at gmail.com
Sun Dec 6 08:49:19 CET 2015

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?

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!

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