VMD-L Mailing List

From: Robert Matthew Fesinmeyer (rmf_at_u.washington.edu)
Date: Wed Oct 03 2001 - 17:42:01 CDT

Hello,

I have a few questions for the group regarding VMD 1.7:

1) The linux box I run VMD on is home-built dual-PIII system running
redhat. When starting, VMD apparently notices this, sending:

      Info) Multithreading available, 2 CPUs detected.

to the console. That said, I've never noticed VMD making use of both
processors simultaneously. Are there portions of the VMD code that are
multithreaded? Should I expect to see any performance improvement from
having the second cpu?

2) I'm quit impressed by VMD's ability to include user-defined graphics in
graphic trajectory output (ala the dials script, for example). I have,
however, had trouble getting the molecule and the graphics in proper
orientation with respect to one another. Is there an easy way to
transform a molecule's coordinates such that a specific bond lies, say,
along the y-axist, with it's midpoint at x=0, z=0?

3) I've noticed that after creating some user defined graphic (say: draw
sphere {0 0 0} radius 10), VMD goes to 100% cpu usage, even though
nothing is being done interactively. Removing the graphic
(Molecule-->Delete) brings VMD back to a normal "resting" cpu usage.
While this isn't a problem with a single sphere, something more complex
(like the Dial script) slows the system down significantly. Is this a
bug, or is there a reason for this?

Thanks for your help,
Matt Fesinmeyer

_________________________
R. M. Fesinmeyer
rmf_at_u.washington.edu
Department of Chemistry
University of Washington