VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 21 2006 - 11:02:49 CDT

Hi,
  There are various scripts around which will align frames by center
of mass, RMSD, etc. For coordination numbers, you might find Lubos Vrbka's
ColorCoord script useful:
  http://www.lubos.vrbka.net/misc.html

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Aug 21, 2006 at 04:26:44PM +0300, Ivan Degtyarenko wrote:
>
> Dear All, if someone has any experience and could share it, I'd really
> appreciate. I'm in process of analyzing the molecular dynamics trajectory,
> the ion solvated in water, and may be somebody has ready solutions, just
> to save time and do not reinvent the wheel. I'm looking for the next VMD
> scripts:
>
> # The first one, which would load a trajectory, go through all frames
> centering them by the center of mass (whole system or some particular
> selection) and save the trajectory to a new file.
>
> # The second script, which could compute the average residence time of
> hydrogen bonds between the ion and water molecules.
>
> # The third one, which would output the abundance of coordination numbers
> of the ion atoms.
>
>
> It would be great to see some code examples, thanks a lot in advance,
>
> YT, Ivan Degtyarenko 

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