[gmx-users] Remove water from trajectory

Mark Abraham mark.abraham at anu.edu.au
Fri Apr 30 10:29:00 CEST 2010

----- Original Message -----
From: Anirban Ghosh <reach.anirban.ghosh at gmail.com>
Date: Friday, April 30, 2010 18:15
Subject: [gmx-users] Remove water from trajectory
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> Hi ALL,
> I just want to convert my trajectory (.trr) to a compressed .xtc format after removing water from it. "trjconv" has to be used for this. I just want to know should I use an index file to exclude the water from the trajectory or is there any other option to be given with trjconv to write out a trajectory without water? Any suggestion is welcome. Thanks a lot in advance.

trjconv with index groups is intended for this purpose. Mostly, the default "SOL" group will suffice, so you just run trjconv in less time than it took to write your email :-)

See http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume


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