From: maria goranovic (
Date: Tue May 10 2011 - 02:27:58 CDT


I know this has been discussed before, but I did not figure out how to reply
to the original thread

So, like many other people here, I want to output a trajectory containing
only water molecules within 5 A of the protein. the obvious problem is that
VMD expects each frame to have exactly the same number of atoms.

However, is there no way to ask vmd to write frames containing the closest N
water molecules to the protein? Has someone written a script for this?

Thank you for helping.


Maria G.
Technical University of Denmark