VMD-L Mailing List

From: Kailee (kaileeamber_at_googlemail.com)
Date: Tue May 29 2007 - 07:43:46 CDT

Dear all,

Thank you for your reply, can I ask how to view the results of volmap? Here
is how I generated the map:
In the selection, I typed "resname O2"; and the molecule used is "top";
volmap type chosen is "occupancy", "avg" for all frames, the output file was
written to "volmap_out.dx" file, after create map, I got the volmap_out.dx
file and also a checkpoint file which is empty.

Then I tried to view the map file, so I loaded volmap_out.dx into the same
molecule, and I changed drawing method to 'isosurface', but nothing appeared
in the screen, and as I changed isovalue, there are something started to
appear, can I ask how to decide how big should the isovalue be?

Also, as the using the volmap, the occupancy is averaged during all frames,
is there anyway to display using different colors for
different occupancy densities during a trajectory? so that I can see at what
region did the gas visited most?

Thank you for any suggestions in advance!

Best regards,
kailee

On 5/28/07, John Stone <johns_at_ks.uiuc.edu> wrote:
>
>
> 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
>