[gmx-users] How can I record only molecule trajectory ?

Justin A. Lemkul jalemkul at vt.edu
Sun Mar 15 16:24:49 CET 2009

Chih-Ying Lin wrote:
> Hi
> The command
> mdrun  -o   traj.trr  -x  traj.xtc
> and then, the two files, traj.trr or traj.xtc will record the
> trajectory of all the molecules of the simulated system.
> How can I record only molecule trajectory with some command?

Use xtc_grps in the .mdp file, or use trjconv after the fact to extract the 
coordinates you want.


> Thank you
> Lin
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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