[gmx-developers] Performance checklist

[Berk Hess]

On 10/12/2012 03:35 PM, Shirts, Michael (mrs5pt) wrote:
> 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.
In itself this is a good point.
But in this context this is not really an issue, because the virtual 
sites remove
the fastest modes and thus decreases the acceleration, making this error
about equally large at 4/5 fs as without vsites at 2 fs.

This would also matter with md-vv, as that has a worse Ekin estimator.

Cheers,

Berk

>
> 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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