[gmx-developers] New Test Set

Shirts, Michael (mrs5pt) mrs5pt at eservices.virginia.edu
Sat Feb 11 18:16:55 CET 2012

> 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.

Agreed.  But picking extremes and random values is not necessarily the way
to do it, because of the 100^10, maybe 0.4995*100^10 are SUPPOSED to crash,
another 0.4995*10^10 are essentially duplicating each other.  Which leaves
100^8 options to test, but random/extreme selection won't necessarily pick
out the right fraction.

A variety of this will likely work work is for EACH parameter, pick out the
1-5 options that really represent something different and should give valid
results, then randomly select from the 100^5 combinations, with rules to
filter out invalid combinations.

I can't seem to edit the wiki, so I can't start a page on this, but perhaps
we should start with the mdout.mdp, and start dissecting exactly what
combinations of options need to be tested, with which different topologies,
and see how many combinations we actually get.

Roland (or other person), perhaps under "Building and Testing" there should
be a third section where we discuss this?

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

But that will require longer physical simulations to detect.

Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu

More information about the gromacs.org_gmx-developers mailing list