From: Axel Kohlmeyer (
Date: Mon May 28 2007 - 10:40:12 CDT

On Sun, 27 May 2007, Kailee wrote:

K> Dear all,
K> I have a trejectory file from AMBER md calculation (.mdcrd file) on gas
K> molecules diffusion into a protein, what I want to do now is to draw a
K> density map of trajectories for all gas molecules across all the frames, can
K> I ask is this what occupancy volmap does or is there any script can do this?

dear kailee,

check out the volume map plugin (Extensions->Analysis->VolMap Tool)
in the latest VMD release.
that should be able to do what you want (and much more)

K> Thank you for any help in advance!
K> Best regards,
K> Kailee

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.