VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Mar 16 2011 - 13:20:42 CDT

On Wed, 2011-03-16 at 17:30 +0000, Peyman Z.Moghadam wrote:
> Hello,
>
> I was wondering if VMD can read and show a pdb file with let's say 500
> configurations each with different number of molecules and then make a movie
> from it? Since the number of molecules are not equal vmd only reads only the
> last configuration!?

not directly. you can split the file into 500 files
(writing a script with a few lines in perl or awk or
python would suffice)

then you'd load them as individual molecules
(use the clonerep plugin to synchronize the
visualizations between them)

and then you can use multimolanim to view on
the screen, but to make an mpeg or similar movie,
you'd have to write a few more lines of tcl script
code inside VMD (similar code fragments have been
posted on this list in the past, if there is sufficient
interest, it might be worth exploring if the multimolanim
and vmdmovie plugins could be combined somehow to
automate the process).

cheers,
    axel.

>
> Thanks,
> //Peyman
>
> 

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