[gmx-developers] New Test Set

David van der Spoel spoel at xray.bmc.uu.se
Sat Feb 11 18:05:58 CET 2012

On 2012-02-11 17:22, Shirts, Michael (mrs5pt) wrote:
>> A while ago I talked about this with Nicu who works with Siewert Jan
>> Marrink. He is a software engineer by training and suggested the
>> following. For each import parameter you take extreme values (e.g.
>> timestep 5 fs and 0.001 fs) and a random value in between.
> I'm not sure this make sense, because lots of things will fail at 5 fs that
> SHOULD fail (Though perhaps we need to make the failure more graceful).  And
> it's not clear that simulations run between 1 and 0.001 fs add any
> information.  So I think that each parameter is a bit more complicated.
That's beside the point. The point is there are 100^10 different mdp 
parameter combinations. The proposed setup makes that all settings are 
tested, although obviously not all combinations.

And about time steps, we previously had problems where a shorter time 
step gave worse energy conservation (also beside the point).

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

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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