[gmx-users] Removing water from a trajectory
Mark.Abraham at anu.edu.au
Wed Jul 14 08:59:30 CEST 2010
On 14/07/2010 4:54 PM, Anirban Ghosh wrote:
> Hi ALL,
> I have a system consisting of protein+lipid+ligand+water which has
> been simulated for 10 ns. Now I want to make a compressed trajectory
> from the original one by keeping only the protein and the ligand. I am
> trying to do so by using trjconv with an index file. But every time
> trjconv is showing the default options and I am not able to select the
> protein and the ligand simultaneously to generate the output. How can
> I do this?
You need to make an index file with a suitable group, and supply that to
trjconv with -n, rather than relying on the auto-generated defaults. See
http://www.gromacs.org/Documentation/File_Formats/Index_File and its links.
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