From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Feb 27 2013 - 10:07:46 CST

Hi,
  Yes, the number of waters (or any atoms) near another selection
will fluctuate throughout the simulation as they jiggle around,
this is completely expected. What is your question?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Feb 27, 2013 at 12:05:46PM +0530, Sindrila Dutta Banik wrote:
> Dear all,
>
> I want to save the coordinates of water molecules which are within 5A of
> substrate PPD from my trajectory. for this I use following:
>
> same residue as (water within 10 of resname PPD)
>
> But the number of water within 5 is changing as I am repeating the same
> exercise. Why this problem comes? Shall I am doing something wrong?
>
> with best regards
> sindrila
>
> --
> Sindrila Dutta Banik
> C/O Prof. A. Chandra
> Project Scientist
> Department of Chemistry
> IIT Kanpur
> UP 208016
>
>
> --
> Sindrila Dutta Banik
> C/O Prof. A. Chandra
> Project Scientist
> Department of Chemistry
> IIT Kanpur
> UP 208016

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078