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

From: Peter Freddolino (
Date: Mon Jul 19 2010 - 20:52:48 CDT

Hi Ian,

On 07/19/2010 09:06 PM, Ian Stokes-Rees wrote:
> Perhaps I didn't explain clearly what I was asking about -- I am
> specifically interested in hearing whether this degree of *un*-aligned
> (i.e. relative to fixed frame of reference) motion was typical for an
> 80k atom system over 1us. If I align the frames, then this motion is
> eliminated.
To directly answer your question, in my experience the type of motion
seen in your movie is pretty typical for simulations on this timescale.
Much more importantly, you should be able to confirm that what you're
observing is physically reasonable (to an order of magnitude) by looking
up diffusion constants for molecules roughly the size of your structure
(keeping in mind that there will be all manner of imprecision due to
severe undersampling, the viscosity of TIP3P water, and the thermostat
that you probably used).
> 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).
Also, I believe there's a "measure cluster" command in development
versions of VMD, although I haven't tried it yet.
> I don't understand why the RMSD isn't reported as exactly zero for the
> reference frame,
Are you sure that the reference frame is being included in the plot for
the stride that you've set? It certainly should be zero...
> and it is unfortunate that the built-in plotter can't
> have the RMSD range fixed, to make successive plots easily comparable.
> 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.
You can always email the author of the plugin and make the suggestion...


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