VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Nov 28 2006 - 16:08:29 CST

On 11/28/06, ivana adamovic <iadamovic_at_gmail.com> wrote:
> Dear all,
>
> Molecule of interest in my simulations is "curved" and its flexibility
> comes from the change in curvature (radius) , or "end to end"
> distance. Can I measure radius of the curvature using VMD?

well, if you can define some set of 'backbone' atoms that define the
curvature, you could write a script that monitors those coordinates
and either -if they are in a straight line- just compute the sum of
the distances, or -if they are more 'zig-zag'- use some kind of fitting
to put a (spline?) function between those and compute the length
of that.

as a raw measure, you can for sure get the 'direct' end-to-end distance.

cheers,
   axel.
>
> Thanks a lot for your help,
>
> Ivana
>
> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.