VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Nov 13 2019 - 00:22:54 CST

I would agree that occupancy would be a logical choice.
The DX files are a simple file format used by a variety of
visualization and analysis tools. There is a basic description
of the file format variants supported by the VMD DX plugin here:
  https://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dxplugin.html

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Nov 08, 2019 at 03:57:35PM -0500, MD Simulation wrote:
> Hello,
> Is it possible to use the volmap function (or gui) to find unoccupied
> volumes (free volume) within a simulation box? I am simulating a polymer
> and would like to understand the void space.
> It looks like the volmap type "occupancy" might work, but I am also
> confused about how to read the dx file format.
> Thanks,
> Stacey 

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