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

From: Peter Freddolino (
Date: Mon Jul 19 2010 - 18:52:20 CDT

Hi Ian,
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 b) colored the
structure by index to give an idea of where the different pieces are.
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. 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. Is the RMSD that you
report all-atom or only for the backbone?


On 07/19/2010 01:18 PM, Ian Stokes-Rees wrote:
> I have run a 1us MD simulation of an 80k atom system (1 fs time step,
> 20k captured frames, every 50 fs) in a water box, and I am surprised
> at how much "gross" movement there is in the structure.
> I am relatively new to MD, so perhaps this should not surprise me, but
> I'd be interested to hear comments from others as to whether or not
> you think this indicates some configuration problem with the initial
> system setup (perhaps params, or minimization/equilibration steps).
> A VDW video of the full 1us simulation (with 1ns per frame, and 1000
> frames total, at 30 fps = 35s video) can be found here:
> The RMSD Trajectory plot (after alignment, and relative to the 500th
> frame) can be found here (in case this provides more insight about the
> overall stability of the system):
> Thanks,
> Ian
> --
> Ian Stokes-Rees, PhD W:
> T: +1 617 432-5608 x75
> NEBioGrid, Harvard Medical School C: +1 617 331-5993

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