VMD-L Mailing List

From: FyD (fyd_at_u-picardie.fr)
Date: Sat Sep 23 2006 - 01:37:06 CDT

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.)