VMD-L Mailing List

From: Marcos Sotomayor (sotomayo_at_ks.uiuc.edu)
Date: Fri Dec 08 2006 - 14:56:45 CST

Hi Paul,

Have a look at the appendices of the NAMD tutorial available at:

http://www.ks.uiuc.edu/Training/Tutorials/
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/index.html
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node21.html

Marcos

On Fri, 8 Dec 2006, Paul T. Bauman wrote:

> Hello,
>
> I'm trying to generate .psf file from my own molecular simulation code and I
> can't find the specific detais of the file format so VMD will accept it. Does
> anyone know where I can look to get the most detailed account of what VMD
> wants in the .psf file?
>
> Basically, I'm visualizing position of atoms as well as covalent bonds using
> a .pdb format. Now, I want to color the atoms according to a real valued
> number that I give it and I gather the best way to hack it is to use a .psf
> file and specify my number as the charge and plot the color according to
> charge. I've found a few examples here and there of a .psf but I haven't
> gotten the format right yet (i.e. VMD errors when it trys to read my version
> of the .psf file). Any help is most appreciated. Thanks,
>
> Paul
>