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

[Mark Abraham]

Sorry, I meant "can be easily done already," not "is done." The
infrastructure to chain a few gromacs tools as in a shell script is now
there, it's just not yet used much yet.

Mark
On Dec 17, 2013 2:52 PM, "Alexey Shvetsov" <alexxy at omrb.pnpi.spb.ru> wrote:

> 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
>>>> --
>>>> Gromacs Developers mailing list
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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
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