VMD-L Mailing List

From: Anne Laustsen (ann3_at_chem.au.dk)
Date: Tue Nov 05 2013 - 03:04:48 CST

Hi,

I have used the VolMap tool in VMD with the following settings:
volmap type: occupancy
resolution: 1 Å
(not use point particles)
Compute for all frames, and combine using: avg

I have a simulation and I am analyzing 4000 frames. I am "tracking" 4 molecules in the same simulation and the space in the simulation box they are occupying the most during the simulations.

My question is about the isovalue, which should be in "whatever units the property is in".
However, I do not know which unit the occupancy is in. If I set the isovalue to 0.06 is this equal to: one of the four molecules is occupying these grid points in 6% of the frames?

Hope you can help.

Anne Kjær Laustsen
Ph.D. student
Biomodelling Group
Department of Chemistry
Aarhus University
Langelandsgade 140
8000-DK