From: Francesco Oteri (francesco.oteri_at_gmail.com)
Date: Mon Jul 19 2010 - 13:39:54 CDT
Il 19/07/2010 19:18, Ian Stokes-Rees ha scritto:
> 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:
>
> http://www.youtube.com/watch?v=IULQt6mER7M
>
> 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):
>
> http://dl.dropbox.com/u/1561496/shared/RMSD-rel-to-frame-500.pdf
>
> Thanks,
>
> Ian
> --
> 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
>
Without deep set-up information is hard to answer you....
Could you send the configuration file? Alternatively sending a link to
read the configuration file is right
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