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

[Szilárd Páll]

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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