VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Apr 11 2011 - 16:47:48 CDT

On Mon, Apr 11, 2011 at 4:53 PM, Vamsee Voora <vkv3_at_pitt.edu> wrote:
> Hello VMD community,
> I have about 100 gaussian cube files and would like to generate a trajectory
> using all these files and visualize the changes in charge density.
> Therefore, either I would need to combine all these files or write a script
> to combine them.
> I did a simple concatenation of files using cat 001.cube 002.cube >>
> traj.cube which obviously doesn't work. So, can you please tell me how to
> combine these files, or the format I should use in order to visualize them

you have to load them with a loop, one at a time and
then you have to use a script to swap the density data set
when you switch to a new frame.

check out section 7.6 in this document that describes a similar case
with data files generated by CPMD.
http://sites.google.com/site/akohlmey/redirect/cpmd-vmd.pdf?attredirects=0&d=1

and have a look at this script.
http://klein-group.icms.temple.edu/cpmd-vmd/files/au-iso.vmd

...and you better do this on a machine with lots of RAM. ;)

cheers,
    axel.

> .
> Thankyou and I will appreciate your help.
> Vamsee
> Vamsee Voora
> Eberly 332
> Ken Jordan's Group: http://www.pitt.edu/~jordan/
> Department of Chemistry
> University of Pittsburgh
> PA 15260
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.