[gmx-users] extracting coordinates from traj.xtc

mah maz mahmaz71 at gmail.com
Thu Dec 3 17:57:06 CET 2015

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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