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

[Justin A. Lemkul]

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:

http://wiki.gromacs.org/index.php/Making_Commands_Non-Interactive

> 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.

-Justin

> -- 
> 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)
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use thewww 
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 

-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================