From: Aaron Oakley (
Date: Tue May 10 2011 - 05:47:47 CDT

Promblem with that is those waters you select will diffuse away from the protein.
Furthermore, if you reselect every, frame you will get a different number of waters
every frame, with differend residue naumers/segid's. You could write out a separate
PDB file for each selection, but this will take up a lot of space compared with a DCD

From: [] On Behalf Of Jernej Zidar []
Sent: Tuesday, 10 May 2011 6:09 PM
To: VMD list
Subject: Re: vmd-l: trajectory of water within 5 A of protein

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