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

[Alexey Shvetsov]

Mark Abraham писал 17-12-2013 06:35:
> 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...

It wasnt. For example genbox doesnt work in 5.0-beta1 it segfaults, and 
tests doesnt cover it

> 
> 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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-- 
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