From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 14 2015 - 10:56:12 CDT

Hi,
  You might be able to approximate the values you're after by using
the volmap occupancy or volmap density commands (or via the volmap
graphical plugin in the analysis portion of the extensions menu).
To compute the volumes you're after you'd likely sample your trajectory
computing the occupancy/density and choose some threshold isovalue
beyond which a region of the space is considered occupied, then count
up the voxels that exceed the threshold and you should have a rough
estimate. There are almost certainly more sophisticated techniques,
but that's a pretty easy one to try and you can directly visualize
the results of such calculations using the Isosurface representation.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jul 07, 2015 at 07:12:29PM +0200, mish wrote:
> Dear all,
> Is possible to calculate volume of the space sampled by ligand in MD
> simulation, either from Amber trajectory or by loading multiple PDB¬ files
> of ligand ( PDB of each conformation of ligand extracted from simulation)
> ? ¬
> In brief, I have an octahedral simulation box, where I am simulation
> binding/unbinding of ligand from a protein. I need to calculate total
> volume of the system (protein+ligand+water) and total volume accessed my
> ligand (within the simulation box) during the MD simulation.¬
> Sincerely,
> Mish¬

-- 
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/