[gmx-developers] [RFC] Test for full cycle of md simulation of small peptide
jalemkul at vt.edu
Mon Dec 16 14:36:28 CET 2013
On Mon, Dec 16, 2013 at 5:34 AM, Alexey Shvetsov <alexxy at omrb.pnpi.spb.ru>wrote:
> 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,
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 ;)
Justin A. Lemkul, Ph.D.
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
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