VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu May 05 2005 - 10:05:16 CDT

Raj,
  VMD doesn't do these things automatically, but it can be used to
make this job much easier since you can write simple script to extract
atom coordinates, make histograms, and do arbitrarily complicated
calculations with the data. I suppose the same could be said of
Matlab or Mathematica or other tools, but what VMD gives you for
something like this is an easy way to select the atoms you care
about and to retrieve the values corresponding to the set of atoms
you want to work with. Once you've done that you can do the math
in VMD or in some external package, whichever suits you best.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, May 05, 2005 at 06:01:56PM +0530, Raj Gupta wrote:
> Hi,
> My system consists of large number of two different species of
> molecules. I want to
> to study the orientational order of one particular type of molecule. I
> need to define a molecular axis and determine its tilt with respect to
> say Z axis. Finally I want to see the distribution of
> tilt by plotting a histogram. Can it be possible to using VMD?
> Otherwise, I have to extract the coordinates from huge pdb files and
> determine the tilt externally and see the distribution. This is
> laborious and time consuming.
> Thanks in advance.
>
> --Raj 

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NIH Resource for Macromolecular Modeling and Bioinformatics
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