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

Inon Sharony InonShar at post.TAU.ac.IL
Mon Oct 27 13:04:30 CET 2008


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.

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?

Inon   Sharony
ינון     שרוני
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[1] http://bugzilla.gromacs.org/show_bug.cgi?id=107)

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