VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 24 2004 - 10:03:40 CDT

Hi,
  It should be possible to write a script that:

a) uniquely identifies your micelles by tagging one of their atom data
   fields with a unique tag for that micelle. Once tagged, you should be
   able to make up an atom selection for each micelle so you can do the
   various measurements you need on each of them, and know which one is
   which at all times.

b) determines which monomer is in which aggregate by some sort of position
   based heuristic, assuming that other parts of the structure are staying
   where they are. I'm not sure what your structure looks like, so this may
   be easy, or it might be quite tricky depending on the details.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Aug 24, 2004 at 12:07:24PM +0000, Andre Farias de Moura wrote:
>
> hi,
>
> I'm trying to describe the interfacial region of
> micelles in aqueous solution and I'm facing some
> problems on the way each lipid molecules should
> be assigned to a unique micelle, because there
> are some monomers exchanging in the course of
> my simulations. that makes it difficult to use
> standard vmd tool to calculate, e.g., center
> of mass for each micelle (there are three of
> them in my simulation box), their radius of
> gyration, the overall diffusion constant of a
> micellar aggregate and so on. all of these
> quantities would need the knowledge of which
> monomer is in each aggregate at any given time
> step, so I would like to know if is there any
> vmd script capable of doing that?
>
> thanks,
>
> andre'
>
> /-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
>
> Dr. Andre' Farias de Moura
>
> /-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
>
> Laboratorio de Quimica Teorica
> Universidade Federal de Sao Carlos
> Sao Carlos - SP - Brasil
>
> /-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
>
> Endereco Atual
>
> Grupo de Quimica Quantica
> Instituto de Quimica de Sao Carlos
> Universidade de Sao Paulo
> Sao Carlos - SP - Brasil
> Telefone: 55-16-3373-8055
>
> /-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/ 

-- 
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