From: Bennion, Brian (
Date: Fri Dec 14 2012 - 17:06:03 CST

From: Axel Kohlmeyer []
Sent: Thursday, December 13, 2012 10:53 AM
To: Bennion, Brian
Subject: Re: vmd-l: visualizing multiframe trajectory simultaneously with multimolecule

On Thu, Dec 13, 2012 at 6:46 PM, Bennion, Brian <> wrote:
> Hello
> I may be making this harder than it has to be. However, I have a multiframe
> trajectory from a protein MD simulation. Each frame has been used to
> calculate a mesh graphics object. As this mesh object changes size and
> shape in time, the only way to visualize these objects in vmd is to use
> multiple molecules.
> at the end of the day I would like to view the protein frames with the
> appropriate mesh overlaid on the protein. Ideally, moving the "slider"
> would select the multiframe molecule frame and somehow select the correct
> graphics molecule.
> Thank you for any suggestions

Extensions -> Visualization -> Multiple Molecule Animation

does this not work?
NO, but you like more details than it doesn't work. The best I can tell you is I can't even test it. It locks up the vmd session and takes most of my cpu cycles until I kill -9 the vmd session.

More details.
mol new test.psf test.pdb test.dcd
6000 frames are loaded into one molecule.

mol new dir1/000000.mesh
mol new dir999/000999.mesh

if the mol new does not find a mesh it loads a blank molecule.
Then I click through Extensions -> Visualization -> Multiple Molecule Animation
It pops up a blank window with the correct label "Multiple Molecule Animation"
Then it just sits there. Maybe there are to many "graphics molecules"?
Is the extension compatible with graphics objects that are called molecules.
Perhaps this is the sticking point?
Anyway I will keep testing with smaller and smaller sets of graphics molecules until I can actually use the extension.

In the meantime, I don't think that "one" slider will advance both the frame number of the 1st molecule and display a single graphics object. Both the slider in the vmd main window and the slider in the multiple molecule extension will have to be coordinated somehow.