VMD-L Mailing List

From: Suman Chakrabarty (suman_at_sscu.iisc.ernet.in)
Date: Sun May 24 2009 - 14:12:06 CDT

Axel Kohlmeyer wrote:
>
>> representation I can show this as slices, but I could not show all the
>> regions together for the whole molecule. I have a feeling that the
>> isosurface representation can probably do this, but I could not figure
>> out how to show the regions with density range "0 to <some cut-off
>> value)" around the solute.
>>
>
> actually, an isosurface shows the the volume enclosed from zero up to
> the specified isovalue. have you considered that if you don't see what
> you expect that the reason may be that you have not computed what you
> think you are computing? this is more often than not the reason why
> people are confused about how to use a representation. you always have
> to keep in mind that VMD is programmed to be incredibly ignorant about
> what a person's intents are and just does what it gets told to do. ;)
>

Thanks for the eye-opener and I have now found out that I was being
stupid not to zoom-in and look into the inner surface that would be
around the solute! Previously I was looking only at the outer surface,
which was essentially the surface of the simulation box. Here comes my
next question: Is it possible not to display the outer surface
(simulation box)? Even when I zoom in, the outer surface is often
disturbingly visible at certain angles.

Second question: How do I calculate the distance between a certain point
on the isosurface and a particular atom of the solute molecule?

Third question: Is it possible to generate the volumetric data per frame
and show it as part of the trajectory animation?

Fourth question: With the volmap type "distance", is it possible to have
a reference group (like solute) and calculate the distance map with the
solvent molecules?

Best regards,
Suman.