Re: 1us simulation of 80k atom system -- how much gross structure movement is expected?

From: Axel Kohlmeyer (
Date: Mon Jul 19 2010 - 21:03:22 CDT

On Mon, 2010-07-19 at 21:06 -0400, Ian Stokes-Rees wrote:

hi ian,


> > You should also try to figure out what structural changes are giving
> > rise to the RMSD changes; clustering analysis would be a good way to
> > start.
> Does VMD provide tools to cluster conformations? I have done a very
> rudimentary study of the two primary domains with RMSD relative to about
> half a dozen points (after aligning all frames around the most static
> domains).

our group is currently working on that.
a first minimal implementation is in the current
VMD development cvs. the implementation is particularly
optimized for long (many frames) trajectories.
i'd be happy to help you get started using it
and giving us feedback.

there also is an external plugin that allows to
visualize the results from other clustering packages.


> I don't understand why the RMSD isn't reported as exactly zero for the
> reference frame, and it is unfortunate that the built-in plotter can't
> have the RMSD range fixed, to make successive plots easily comparable.

like many of the VMD plugins, it is implemented by somebody
to satisfy a particular personal need and programmed to the
taste and capability of the author. typically, people writing
these plugins are not formally trained as programmers, and
sometimes not even very experienced (everybody has to start
somewhere). as you already experienced, keeping the status of
a plugin in sync with the currently available molecules is
a particularly difficult to program item. several plugins
have problems with that, and it took my quite some time and
feedback from users to program it without (apparent) failures
for the GUI plugins that i have written.

feedback is always appreciate, code even more. in general, it
is a good idea to look up the original author and make direct
contact, but for some of the older plugins, that might be difficult.
people move on quite quickly in our business.


> I can, of course, save the data, import it into another program
> bit-by-bit, and then plot these with a fixed Y-axis (RMSD, starting from
> zero), but it would be so much easier if this had the y-axis fixed to
> start at zero, and the option of auto-scaling the maximum, or fixing the
> maximum RMSD value.
> Thanks for your input.
> Ian

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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