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

Alexey Shvetsov alexxy at omrb.pnpi.spb.ru
Mon Dec 16 15:05:57 CET 2013

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, 
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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