From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Sep 22 2006 - 14:18:16 CDT

gustavo,

you have multiple options depending on what format you have
the charge information in. i assume that you have the charges
for the QM subsystem as partial charges that vary over the trajectory. right?

that information you can actually store in the User field, since this data
is per-frame. so in essence you need to combine the recepies for
the argon and the buckyball example to do this.

if you first load the corresponding amber topology files, you'll also
get the partial MM charges embedded into your system. now
you can do two representations for the QM and the MM atoms
and use the Charge colorization on the MM and User for the QM
atoms and you should get something along the lines what you
desire. of course you can make even more restrictive selections.

i'm very busy right now, but if you'd get back to me in a
couple of weeks, i'd be more than happy to include something like
this as an additional example into the tutorial. ...and we could also
use such a trajectory for a demo on the IR-spec plugin and a dipole
visualization plugin that was added to vmd shortly after the release
of version 1.8.5 (it is available from biocore).

cheers,
   axel.

On 9/22/06, Gustavo Seabra <gustavo.seabra_at_gmail.com> wrote:
> Hi,
>
> I have a large system, and I have charge data for just part of it
> (it's a QM/MM simulation). How can I use VMD to visualize the charges
> only in this part, or even better, only in specific atoms? (It could
> be with a change in color, or whatever other means people use for
> that.)
>
> (I saw the demo in Axel Kohlmeyer web page, but there he used a system
> of only 3 atoms. What I have are Amber files using ~5000 atoms, for
> which I have charges for only 140.)
>
> Thanks,
>
> Gustavo.
>
>

-- 
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Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
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