VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Sep 06 2006 - 10:54:30 CDT

On 9/6/06, Silvina Matysiak <silvina_at_rice.edu> wrote:
> Hi,
>
> I need to make a movie of water simulations
> and in each step (frame) I need to consider a different list of atoms
> for a representation.
> Does anybody knows how to do this?

there would be more or less two ways.
a) if you can describe the selection criterion
with the VMD selection language, you just
create a representation for that and make
sure that under the trajectory tab, you have
the 'Update Selection Every Frame' checkbutton
activated.
b) you compute the list of atoms separately
and then store either a -1 or a 1 in the corrsponding
'user' field and then use a selection 'user > 0' to
show only those atoms.

http://www.theochem.rub.de/~axel.kohlmeyer/cpmd-vmd/part3.html#chap5_sect3
has an example for how to store data in the user field
via tcl in VMD, and
http://www.theochem.rub.de/~axel.kohlmeyer/cpmd-vmd/part3.html#chap5_sect4
and example for reading data from an external file.

cheers,
   axel.

>
> Thanks,
>
> Silvina
>
> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.