VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Sep 07 2004 - 16:27:38 CDT

Hi,
  Rather than making your own format, I'd suggest that you use one of the
many existing molecule/trajectory file formats so that you can work with
whatever software suits your needs. One easy-to-code format is the XYZ
format described here:
  http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/xyzplugin.html

VMD doesn't support all of the features of that format, but it'll get you
started and would allow expansion later. There are numerous other
file formats that might be better suited to your task, but XYZ is an
easy, fairly common file format to write output code for.

VMD doesn't currently read the "extra" data from XYZ files because
there's no way to guess their meaning. I intend to make VMD read these
into extra user-data fields at some point, but presently this is not the case.

VMD doesn't presently have a means of displaying velocity vectors built-in,
but that probably wouldn't be too difficult to add, if necessary. It can
easily be done with scripting with the existing versions of VMD.

  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Sep 05, 2004 at 12:04:40PM -0500, Paul Christopher Millett wrote:
> I just downloaded the software and it looks great. I use a self written MD
> program. I simply need to be able to visualize the atoms as balls and the
> velocity vectors of each atom. Which format would you suggest for output
> files? The basic layout I was thinking is:
>
> N (number of atoms)
>
> x,y,z,vx,vy,vz,id (these are the position coord., velocity components, and
> an integer to describe the atom)
>
>
>
> I am working with crystalline atomic systems (not protein structures, etc.).
> I was looking at the XYZ file format and this seems to work except I cannot
> use any other information about the atoms. How do I name the XYZ files
> (perhaps: file_name.xyz)? Thank you very much for your time.
>
>
>
> Paul Christopher Millett
>
> PhD Student, Computational Mechanics Lab.
>
> University of Arkansas
>
> 4190 Bell Engineering Center
>
> Fayetteville, AR 72701
>
> work: 479-575-2229, cell: 479-466-5731
>
>
>
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078