VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Dec 19 2005 - 16:51:29 CST

Hi,
  For a), did you mean "get" rather than "set"? If you really mean "set",
then you'll need to first calculate the centroid (using the 'measure center'
command), then transformation(s) to move it to the desired location.
For b), you can use the 'veclength' command to measure the distance.
In order to compare for all frames, you'll make the atom selections for
the reference frame and "current" frame, and you'll use the "$sel frame $x"
command to update the current frame you're comparing against the reference
frame. There are a few trajectory processing scripts in the VMD script library
that should be helpful to look at.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Dec 16, 2005 at 01:37:07PM -0600, Michel Espinoza-Fonseca wrote:
> Hi all,
>
> I was wondering if any of you know how to: (a) set the coordinates of the centroid of a given aromatic ring and (b) how to measure the distance between two centroids over time using VMD.
>
> All comments will be really helpful.
>
> Thanks a lot!
>
> Michel
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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