VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 23 2009 - 15:04:06 CST

Hi,
  The easiest way to do this would be to load your coordination numbers
into one of the per-atom-per-timestep "User" data fields in VMD. This
requires doing a bit of scripting, but there are a number of examples
of ways to use the User fields in Axel's CPMD/VMD tutorial:
  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part4.html#chap6_sect4

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Feb 22, 2009 at 11:42:19PM -0500, Yang, Shaorui wrote:
> I want to color the atoms of a metal nanowire by the coordination number
> of atoms to see the presence of some defects like dislocations. I can use
> LAMMPS to compute the coordination #s of each atom and dump them into the
> trajectory file. But the problem is how can I let VMD to identify the
> LAMMPS trajectory file with a different format with the default setting. I
> would appreciate if anyone can give me some suggestion on how to do that.
> Thank you all.
>
>
>
> Regards
>
> Shaorui Yang
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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