From: John Stone (
Date: Sat Nov 23 2013 - 00:39:53 CST

  I believe that your interpretation is correct and that a 6%
occupancy would correspond to an isovalue of 0.06.

  John Stone

On Tue, Nov 05, 2013 at 09:04:48AM +0000, Anne Laustsen wrote:
> Hi,
> I have used the VolMap tool in VMD with the following settings:
> volmap type: occupancy
> resolution: 1 AA
> (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 Kjaer Laustsen
> Ph.D. student
> Biomodelling Group
> Department of Chemistry
> Aarhus University
> Langelandsgade 140
> 8000-DK

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