[gmx-developers] [RFC] Test for full cycle of md simulation of small peptide

[Mark Abraham]

Hi,

"Does not segfault" is easily done already with the integration test
machinery recently added. Anything more sophisticated needs a way to
examine the results and compare with what was expected...

Mark
On Dec 17, 2013 2:51 AM, "Szilárd Páll" <pall.szilard at gmail.com> wrote:

> I agree, there is value in such a test even if it is used to only
> check that the tools used work. Of course, providing somewhat stricter
> checks on what "works" mean should be the goal, but even if the first
> version does not do this, I suggest adding such a test.
>
> Cheers,
> --
> Szilárd
>
>
> On Mon, Dec 16, 2013 at 3:05 PM, Alexey Shvetsov
> <alexxy at omrb.pnpi.spb.ru> wrote:
> > Justin Lemkul писал 16-12-2013 17:34:
> >
> >> On Mon, Dec 16, 2013 at 5:34 AM, Alexey Shvetsov
> >> <alexxy at omrb.pnpi.spb.ru> wrote:
> >>
> >>> Hi!
> >>>
> >>> May be it will be good to have small test that emulates full cycle
> >>> of md system preparation and run (just for few dozens of steps for
> >>> each mdrun). As small peptide we can use e.g. speptide, cpeptide or
> >>> may be even trp-cage. This will allow to catch bugs in preparation
> >>> utils (e.g. genbox, genion)
> >>
> >>
> >> That could be good, but how robust would such a test be?  Energies
> >> could vary quite a bit based on ion placement (which by default is
> >> random) and I have even seen cases where genbox adds a slightly
> >> different number of waters to identical solutes in identical boxes, so
> >> the topology may not even be consistent.  This is fairly rare, but I
> >> do get people panicking when doing my tutorials if they somehow get
> >> one fewer water molecule in their box ;)
> >>
> >
> > I think it will be test to check it all tools works as expected without
> > crashes and segfaults.
> >
> >
> >> -Justin
> >>
> >> --
> >>
> >> ==========================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 601
> >> University of Maryland, Baltimore
> >> 20 Penn St.
> >> Baltimore, MD 21201
> >>
> >> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >>
> >> ==========================================
> >
> >
> > --
> > Best Regards,
> > Alexey 'Alexxy' Shvetsov
> > Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina,
> > Russia
> > Department of Molecular and Radiation Biophysics
> > Gentoo Team Ru
> > Gentoo Linux Dev
> > mailto:alexxyum at gmail.com
> > mailto:alexxy at gentoo.org
> > mailto:alexxy at omrb.pnpi.spb.ru
> > --
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