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

From: Andrew Emerson (
Date: Tue Jul 20 2010 - 05:09:05 CDT

Dear Ian

I have also done a 1 microsec simulation and the protein moves quite a
lot , so much in fact that the unprocessed dcd doesnt make a good movie.
Given the timescale I think this behaviour is reasonable, well anyway my
biochemist collaborators arent too worried.

BTW, for RMSD and cluster calculations you might find analysis programs
such as carma or wordom useful. I found carma particularly convenient
also for removing the centre of mass motion and solvent from the
original dcd for inputting into VMD to create a usable animation, for

best wishes
Andy Emerson
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

Dr Andrew Emerson
CINECA (High Performance Systems)
via Magnanelli, 6/3
40033 Casalecchio di Reno (BO)-ITALY
tel: +39-051-6171653, fax: +39-051-6137273

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