VMD-L Mailing List
From: Jeffrey Potoff (jpotoffx_at_gmail.com)
Date: Fri Feb 08 2013 - 09:56:22 CST
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I suggest the following:
1. Write a script or C/C++ program to convert your XYZ file to PDB format.
2. Pad the PDB file so you always have a constant number of entries.
3. Use the occupancy field to denote whether an entry is real or a filler.
4. For the radius, you could map radius from the XYZ file to an atom
type (which would then be defined in the PDB field). Diameters of atom
types can be defined in VMD, so you can create whatever mapping you need.
Hope this helps,
Jeff
On 02/08/2013 07:55 AM, Gavin Melaugh wrote:
> Hi All,
>
> I have been using VMD for the last 3 years to analyse trajectories from
> molecular simulations.
>
> Recently I have started a new project looking at the population
> dynamics of
> bacterial growth. Since I am used to using VMD I was wondering the
> following:
>
> 1) Can I load xyz configuration files into VMD, in which the number of
> particles
> (bacterial cells) is different in each configuration file.
>
> 2) Also if 1) can be achieved, is there also a way of defining the
> radius of
> each individual particle. The output from my simulation gives xyz
> files with the following format
>
> agent x y z radius
> 1
> 2
> 3
>
> I can generate movies from the simulations but I just find that I can
> not interact with them in the way that I am used to.
>
> Many Thanks in Advance
>
> Gavin
>
-- ====================================================================== Jeffrey J. Potoff jpotoff_at_wayne.edu Associate Professor Wayne State University Department of Chemical Engineering and Materials Science 5050 Anthony Wayne Dr Phone:(313)577-9357 Detroit, MI 48202 Fax: (313)578-5815 http://potoff1.eng.wayne.edu ======================================================================
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