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

From: Ian Stokes-Rees (ijstokes_at_hkl.hms.harvard.edu)
Date: Mon Jul 19 2010 - 12:18:55 CDT

 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):




Ian Stokes-Rees, PhD                       W: http://hkl.hms.harvard.edu
ijstokes_at_hkl.hms.harvard.edu               T: +1 617 432-5608 x75
NEBioGrid, Harvard Medical School          C: +1 617 331-5993

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