[gmx-users] Removing water from a trajectory

[Mark Abraham]

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.

Mark