VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jun 09 2010 - 11:49:55 CDT

michael,

On Wed, Jun 9, 2010 at 6:25 AM, Michael Doig <m.doig_at_sms.ed.ac.uk> wrote:
> I am wondering if it is possible to assign partial charges in VMD.

yes. example:

set sel1 [atomselect top "name OW"]
$sel1 set charge -0.84
set sel2 [atomselect top "name HW"]
$sel2 set charge 0.42
$sel1 delete
$sel2 delete

> I read in an xyz coordinate file - I want to be able to select certain atoms
> and assign a partial charge to these atoms. I then use topotools to output
> my LAMMPS datafile.

correct. you have to use atom style full or charge
to get the charges written to the data file.

> Is it possible to assign partial charges to selected atoms in VMD, and have
> this information incorporated into my LAMMPS data file which I produce using
> topotools.

topotools will use whatever information is available and supported
by the atom style that you select for writing out the data file.

cheers,
     axel.

> Thanks,
> Michael Doig
>
> ---
> PhD student
> School of Chemistry
> University of Edinburgh
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.