From: Axel Kohlmeyer (
Date: Sun May 24 2009 - 14:32:20 CDT

On Mon, 2009-05-25 at 00:42 +0530, Suman Chakrabarty wrote:

> 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.

you can use clip planes.

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

please explain - in terms that are not "descriptive" - how would
you determine this point in the first place?
depending on whether that is possible, you have a chance to
script it. based on previous discussions on similar subjects
on this list, i'd doubt it, though. you have to keep in mind,
that the volumetric data set is on a rather coarse grid and
that the isosurface is a smooth interpolation between those
data points, so an accurate determination is not possible.

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

not directly, but you can script it. for an example, see:

> 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?

no, please read the volmap distance documentation.


> Best regards,
> Suman.

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.