From: Jernej Zidar (
Date: Tue May 10 2011 - 03:09:38 CDT

I would use this selection: within 5 of protein (check the syntax)

Then I would save the trajectory with the above selection.

Jernej Zidar

On 10.5.2011, at 9:27, maria goranovic wrote:

> Hi
> 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
> --
> Maria G.
> Technical University of Denmark
> Copenhagen