[gmx-users] splitting a trajectory according to atoms using trjconv

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 27 13:19:34 CET 2008

Inon Sharony wrote:
>  Hi,
> I read GROMACS bugzilla report of bug 107
> (http://bugzilla.gromacs.org/show_bug.cgi?id=107)[1]  and have to
> admit that I have no experience using trjconv.
> I really just need a push in the right direction -- I can't seem to
> find any decent explanation on how to use trjconv for this purpose
> anywhere on the net.
> What I'm trying to do is take a trajectory file I generated, and
> perform a trajectory analysis of two specific atoms in the molecule.
> Since g_traj only takes one index group, this is a problem. In
> particular, I want to automate the process and use non-interactive
> command-line calls.

Have a look at this:


> I think I should split the entire-molecule's-trajectory so that I
> have a separate trajectory file for each atom I would like to look at,
> and then serially run g_traj for each atom-trajectory.
> How do I use trjconv to split one trajectory file into a few,
> according to index groups or atoms?

Just make the index groups you wish, and pass them to trjconv with -n.


> -- 
> Inon   Sharony
> ינון     שרוני
> +972(3)6407634
> atto.TAU.ac.IL/~inonshar
> Please consider your environmental responsibility before printing
> this e-mail.
> Links:
> ------
> [1] http://bugzilla.gromacs.org/show_bug.cgi?id=107)
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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