Re: [AMBER] On the usage of the position restrains during equilibration

From: Jason Swails <jason.swails.gmail.com>
Date: Sun, 22 Jun 2014 15:34:06 -0400

On Fri, Jun 20, 2014 at 9:48 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> ‚Äč\
> I'm a sole fan of quickly generating a few long vacuum trajectories at low
> temperature at the beginning, just for the sake of fiddling with some
> controls on the movie, with no big investment for a few minutes or so :-).
>

I'd not suggest vacuum simulations ever unless you are specifically trying
to model vacuum behavior and you are well versed in its limitations.
 Systems behave qualitatively differently in vacuum and solution (it's
solution effects at biological temperatures that drive the native folds of
any biomolecule).

While vacuum simulations can in theory be done more efficiently than GB
calculations, in practice this is no longer true for Amber. Only sander
can run vacuum simulations -- they are not supported by either pmemd or
pmemd.cuda. So in practice you can run a GB calculation (which will be far
more representative than a vacuum simulation for any biomolecule in
solution) 10 to 100x faster in pmemd.cuda than you can run a vacuum
simulation with sander.

All the best,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Jun 22 2014 - 13:00:03 PDT
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