[gmx-users] extract protein and counter ions from trajectory

[Martin Höfling]

Am Freitag, 12. September 2008 schrieb sarbani chattopadhyay:

>                     I want to know is there any way to extract the
> coordinates of both the protein and counterions from the trajectory while
> writing the "pdb" file ie. I don't want the water molecules but only the
> protein and the counter ions.
>  I did not see that option wile trying to generate the pdb files.
> Is there any way of doing this?

You can create an index file, containing a union of both groups and then 
provide this to trjconv.

Best
	Martin