VMD-L Mailing List

From: saam (saam_at_ks.uiuc.edu)
Date: Fri Oct 23 2009 - 08:39:32 CDT

Dear Ignacio,

>> compiling a single plugin for dynamic linkage is straightforward.
>> you don't really have to use the full VMD build infrastructure
>> for that. there should be some info in the developer docs online.
>> i can also send you a makefile that i've been using for the
>> HOOMD plugin (which is not part of the VMD distribution), that
>> works well on different kinds of linux machines.
>
> I would appreciate it if you could send me the necessary instructions to having it started. I'm not a newbie at compiling source packages, but I must be doing something wrong.

Tell us exactly where you got stuck. I hope you are working under
Linux, other wise you have no chance I think. Have you seen The
instructions how to compile plugins in the programmers manual? Which
step doesn't work for you?

> Regarding the orbital representation, I would like it to draw simultaneously positive and negative parts, with different colours, but with the same other settings. Currently I can get it in two ways:
>
> - Duplicate the representation, change the sign of the isosurface value and change the colour. The downside is every change I want to make I have to make it in the two representations.

Note that the plugins have no influence on the representations. They
only populate data structures in VMD. In order for the Orbital rep to
work the basisset and wavefunction coefficient data have to be
present. A future version of VMD might have a more sophisticated
Orbital rep that allows you to select both signs at once.

> - Create cube files with the amplitude and its absolute value. Use the second in an isosurface representation, coloured by valume with the first. This has all the shortcomings of cube files, and requires preprocessing and GLSL capable display.

You can do that but it's a pain.

> Would it be possible to add an option for this kind of representation to the orbital representation GUI? Or maybe I'm missing it already?

You can't change the orbital rep withot digging deep into VMDs code. See above.
My understanding from your previous emails is that you are considering
to develop a molden plugin. I will help you with this. Currently I'm
working on a simple example of a QM plugin that can be used as a
template for other plugins. Should be done in a few days hopefully.
Meanwhile you should figure out how to compile the plugins. As I said
above, tell us exactly wha you are doing and where you get stuck. Then
we can help.

Jan

> Thanks,
> Ignacio
>
>
>
>
> 

-- 
****************************************
Dr. Jan Saam
Theoretical and Computational Biophysics Group 3061 Beckman Institute
University of Illinois
405 N. Mathews Ave
Urbana, IL 61801
Phone: (217) 244-1928
Fax:   (217) 244-6078
saam_at_ks.uiuc.edu