VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 29 2007 - 00:21:48 CDT

Hi,
  I'm not aware of any existing scripts for this purpose, you may
have to develop your own. You can probably use some of the other VMD plugins
for boundary crossing math etc.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Aug 23, 2007 at 11:07:49AM -0400, zhenlong li wrote:
> Dear all:
>
> My system starts from homogeneous dispersion of surfactants in solution.
> And the DCD file records the whole process of micellerization. Now I define
> that any molecule pair within certain distance belongs to the same
> aggregation and try to get information such as aggregation numbers, numbers
> of aggregation, lifetime of aggregations, residence time of unimers in
> micelles every timestep. I just wonder if there is any script or tool to do
> this, or any good idea to deal with aggregations crossing the boundaries.
> Thanks in advance.
>
> best,
> Zhenlong 

-- 
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