VMD-L Mailing List

From: Paweł Kędzierski (pawel.kedzierski_at_pwr.wroc.pl)
Date: Thu Oct 20 2011 - 03:06:30 CDT

Dear Bruno,

W dniu 19.10.2011 16:04, Bruno Luís Pinto de Oliveira pisze:
> Dear all,
>
> Recently I published a post asking how to visualize an alchemical
> transformation but no one answered me.
>
> Probably is a basic question, however I still do not know how to
> visualize it.
>
> I searched in the VMD mailing list and in the manual and I didn´t find
> any information about this subject.
>
> In my particular case I have a compound that is a organic molecule
> coordenated to a metal core (Re(CO)3). In the FEP simulation I am
> vanishing the metal core. The calculated results are in good agreement
> with the experimental.
>
> What I would like to know now is if it is possible to visualize with
> VMD the Re(CO)3 metal core disapearing???
>
> Is it possible???
I have no personal experience with such visualizations but since you
didn't get other answers, let me share my thoughts.
I think it is possible provided you can load the trajectory into VMD,
but AFAIK there is no option to achieve it directly and you would need
to do some scripting.
VMD supports two scripting languages: Python and Tcl but the former is
not available in Windows version and the Python API is less tested and
more buggy than Tcl so it may be a better idea to learn Tcl scripting.
If you (will) use VMD regularly it is a good investment anyway. For
basic syntax there are many tutorials on the web, and the VMD API is
well described in the VMD User Guide.
The idea I would propose is to make the disappearing part becoming
thinner and/or more transparent during the trajectory animation:
- make a separate graphical representation for the disappearing part.
Make sure it uses a material separate that the rest of the system if you
want to change its transparency;
- write a Tcl function which will multiply the atom and bond radii
and/or the material transparency of the (metal core) representation by a
factor from 1 to 0 depending on the current trajectory frame;
- install this function as a callback which will be automatically called
on frame advance or on screen update.
Greetings,
Pawel Kedzierski

>
> I have made myself clear?
>
> Tks in advance
>
> Bruno
> .....................................................................................................................................................
>
> Bruno L. Oliveira
> Radiopharmaceutical Sciences Group
> Chemistry Department , ITN
> http://www.itn.pt/sec/qui/qir/uk_qir_index.htm
> http://www.boliveira.com