From: Eduard Schreiner (
Date: Tue May 10 2011 - 09:51:13 CDT

Hi Maria,

I have a proc which will do what you want (ww_nearest.tcl). The file
get_closest.tcl shows how it can be used.
1. it is SLOW for large systems and certainly can be improved
2. it's certainly not the best way to do that, but it seems to work
for me (I tried it for water and for ions; I did not use it for
anything serious, though)
3. it is not extensively tested

Check it out and let me know how that works for you.

Maybe somebody knows a better way; any suggestions/improvements are appreciated.

let me know if you have any trouble with it


On Tue, May 10, 2011 at 9:27 AM, 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