[gmx-developers] Performance checklist

[Shirts, Michael (mrs5pt)]

Hi, all-

> I added a performance check-list on the Gromacs site:
> http://www.gromacs.org/Documentation/Performance_checklist

The one concern I have about recommending 4 to 5 fs steps for virtual sites
is that the ambiguity about what the real kinetic energy is (because we are
using estimators for the kinetic energy when we use either leapfrog or
verlet) becomes worse as the step size becomes larger. This means the fact
that a system reports itself to be at the correct temperature is not
necessarily conclusive.

This is a situation where going through and doing an ensemble check to make
sure the potential energy distributions are properly valid for the desired
temperature would be a good study to do -- I'm happy to help someone set one
up using the checkensemble tools I've developed, though I don't have the
time to do it all myself.  Of course, maybe I've missed some careful checks
that have been done on that system in the meantime, and this level of
checking has been done already.

As a semi-aside, note that some of these concerns might be fixed by
implementing some sort of hybrid MD/MC.  I'm still arguing for (and ready to
help organize) for 5.0 a more general integrator class that supports (as
default) straight MD, but can also handle more generate MC moves, which
would include hybrid MD and allow relatively large time steps w/o any errors
in the distribution.

Best,
~~~~~~~~~~~~
Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
(434)-243-1821


> From: Berk Hess <hess at kth.se>
> Reply-To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Date: Fri, 12 Oct 2012 15:21:54 +0200
> To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Subject: [gmx-developers] Performance checklist
> 
> Hi,
> 
> I added a performance check-list on the Gromacs site:
> http://www.gromacs.org/Documentation/Performance_checklist
> 
> If something is unclear or you have something to add, pease tell me.
> Note that about half of the points on the list only apply to version 4.6.
> 
> Cheers,
> 
> Berk
> 
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