VMD-L Mailing List

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Mon Aug 30 2010 - 11:28:45 CDT

Hi all,

The current system VMD uses for protein secondary structure
assignment, while it works, has shortcomings. One is performance: when
dealing with large trajectories, the initial assignment performed by
the sscache script is fairly slow. One idea would be to take advantage
of multicore machines by running stride on multiple frames at once.
The issue here is that VMD itself knows only one secondary structure
assignment per molecule - right now that's handled fully in Tcl by
scache. After a quick look at threads in Tcl, I've decided that it
might not be a good idea to parallelize on that side. So it seems that
as long as VMD does not have secondary structure as per-timestep data,
we're stuck.

Another idea is to avoid writing to disk the data fed to Stride -
either using named pipes, or requesting from the authors the
permission to link Stride into VMD. I am not sure how much performance
would be gained by doing this though - it could be that disk caching
reduces the performance impact of the current implementation to almost
zero.

I'm sure others have been thinking about this for a while, so I'd like
to hear your perspective. I can name at least two people who are going
to answer this :-)

Cheers,
Jerome

PS: unsubscribe vmd-l. Seriously guys. And namd-l too. I mean it.