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

Martin Höfling martin.hoefling at gmx.de
Fri Sep 12 13:18:54 CEST 2008

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.


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