VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Nov 23 2013 - 00:39:53 CST

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

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

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 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/