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

From: Ian Stokes-Rees (
Date: Mon Jul 19 2010 - 20:06:05 CDT

On 7/19/10 7:52 PM, Peter Freddolino wrote:
> It would be a lot easier to get a feel for what is going on if you a)
> aligned the frames prior to making the movie, and

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

> b) colored the structure by index to give an idea of where the
> different pieces are

On this point, I had been asked by my PI to obfuscate details of the
structure. It has not yet been published, and is the result of a few
years of work. As such, a single-color VDW image seemed the best
representation to capture the gross structural movement in a fixed frame
of reference over 1 us.

> 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

> My bet is that you're exploring two or more distinct conformations
> separated by a low barrier, given that you return to sub-2 A RMSDs for
> awhile in the middle of the trajectory.

Yes, that appears to be what happens. Two domains open and close.

> Is the RMSD that you report all-atom or only for the backbone?

Backbone only, I believe.

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.
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.


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