VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Sep 23 2006 - 03:00:55 CDT

Francois,
  Did you try the "charge" coloring method yet?

  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Sep 23, 2006 at 08:37:06AM +0200, FyD wrote:
> Dear Axel, dear All,
>
> And what about visualizing charge _values_ in a 'simple' file like for
> instance .pqr or .mol2 file ? How to do that with VMD ?
>
> Thanks, Francois
>
> >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).
>
> >>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.)
> 

-- 
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