VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon May 28 2007 - 15:34:23 CDT

Hi,
  Yes, the volmap command can do this for you. The occupancy
volmep essentially averages the occupancy of each of the voxels
in the map over a trajectory, for the given selection. If a
voxel is occupied, then for that frame, it gets a "1", if not,
it gets a "0", and the occupancy is summed over all frames
and renormalized at the end.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, May 27, 2007 at 06:54:12PM +0100, Kailee wrote:
> Dear all,
>
> I have a trejectory file from AMBER md calculation (.mdcrd file) on gas
> molecules diffusion into a protein, what I want to do now is to draw a
> density map of trajectories for all gas molecules across all the frames, can
> I ask is this what occupancy volmap does or is there any script can do this?
> Thank you for any help in advance!
>
> Best regards,
> Kailee 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078