VMD-L Mailing List

From: FyD (fyd_at_u-picardie.fr)
Date: Mon Sep 25 2006 - 04:47:27 CDT

Quoting John Stone <johns_at_ks.uiuc.edu>:
>
> Did you try the "charge" coloring method yet?

Yes, but the charge _values_ are NOT displayed, colors are displayed.
Is it possible to display the charge _values_ (in fact, a label like
the atom name) ?

Thanks, Francois

>> And what about visualizing charge _values_ in a 'simple' file like for
>> instance .pqr or .mol2 file ? How to do that with VMD ?
>
>> >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.)