[gmx-developers] Performance checklist

[Shirts, Michael (mrs5pt)]

> 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 is a reasonable theory, that is likely right.  It should be tested
though, rather than assumed.
 
> This would also matter with md-vv, as that has a worse Ekin estimator.

Agreed.  Quantifying this amount would be useful.

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



> 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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>