From: Josh Vermaas (
Date: Mon Jan 05 2015 - 10:49:39 CST

Hi Yeping,

You'll need to update your atomselection at every frame (its an option
under the trajectory tab of the graphical representations window).
-Josh Vermaas

On 01/03/2015 09:13 AM, Sunyeping wrote:
> Dear all,
> I want to show all water molecules within 3.5A of a particular
> residue in the protein through out a MD trajectory in VMD. In
> Graphical representations dialogue box, I created a representation
> with the atom selection being "water and within 3.5 of segname P3 and
> resid 3". This operation did show water molecules around this protein
> residue, but this atom selection applied just to the frame which was
> showed in VMD when the atom selection was made but not for all the
> frame. When I changed the frame showed in VMD, I could observe these
> water molecules left far away from that protein residue. So how can I
> show just the water molecules around the reside for all the frames?
> Yeping Sun
> Institute of Microbiology, Chinese Academy of Sciences