[gmx-developers] [gmx-core] removal of encad and gmx FF in 5.0?
Thomas Piggot
t.piggot at soton.ac.uk
Tue Feb 18 18:08:43 CET 2014
Will do, thanks. Nice to meet you yesterday, by the way!
Cheers
Tom
On 17/02/14 19:57, Erik Lindahl wrote:
> No idea since I'm not using it myself - talk to Eric Sorin at
> eric.sorin at csulb.edu <mailto:eric.sorin at csulb.edu> who asked about it.
>
> Cheers,
>
> Erik
>
> On 17 Feb 2014, at 11:35, Thomas Piggot <t.piggot at soton.ac.uk
> <mailto:t.piggot at soton.ac.uk>> wrote:
>
>> Hi Erik,
>>
>> What was the issuse you metion with the BSC0 parameters (I take it
>> you are referring to the contributed force field that I added to the
>> GROMACS website)? I tested the conversion of the new dihedrals by
>> looking at single-point energies between AMBER and GROMACS and they
>> matched up. If there is a problem, I would like to know so as to be
>> able to take a look at it.
>>
>> Cheers
>>
>> Tom
>>
>> On 14/02/14 16:47, Erik Lindahl wrote:
>>> Hi,
>>>
>>> I would strongly prefer that we do NOT ship forcefields that haven't
>>> had (1) plenty of testing, (2) somebody named who is responsible for
>>> each of them, (3) specifics on how to repeat the testing.
>>>
>>> The second we ship something with official Gromacs people will start
>>> using it, and then they will instantly blame Gromacs if there are
>>> errors in the force field. This is exactly why we have separate
>>> contributed sections, to make it clear it is not our responsibility.
>>>
>>> BSC0 is a concrete example: It was only a week ago I got a mail from
>>> Eric Sorin about BSC0 not reproducing some results. For a
>>> contributed force field that is the problem of the contributor. If
>>> we are shipping it with Gromacs-5.0, it will tarnish our reputation.
>>>
>>> Cheers,
>>>
>>> Erik
>>>
>>>
>>>
>>> On 14 Feb 2014, at 08:38, Rossen Apostolov <rossen at kth.se
>>> <mailto:rossen at kth.se>> wrote:
>>>
>>>>
>>>> On 14/02/14 17:12, Mark Abraham wrote:
>>>>> Removing encad and gmx sounds good. Probably don't have time to
>>>>> rip out the code that supported encad.
>>>>>
>>>> I can look at that.
>>>>
>>>>> We're happy to add forcefields that are used by more than one
>>>>> person, have been extensively tested, have an associated
>>>>> publication record, etc. Any particular suggestions, Alexey? Others?
>>>>>
>>>> I vote also for Stockholm lipids, it can be quite useful, but
>>>> hasn't got much publicity.
>>>>
>>>> Rossen
>>>>
>>>>> Off the top of my head, Charmm36 would be an obvious thing to add.
>>>>> My reservation here is that there's not really ever been a good
>>>>> way to run CHARMM-style non-bondeds in GROMACS. I suspect this
>>>>> will change in 5.0 with Verlet-kernel support for switch
>>>>> functions, but perhaps a fully validated forcefield and workflow
>>>>> port for 5.1 would be a good joint project. Thoughts, Justin?
>>>>>
>>>>> Mark
>>>>>
>>>>>
>>>>> On Fri, Feb 14, 2014 at 4:39 PM, Alexey
>>>>> Shvetsov<alexxy at omrb.pnpi.spb.ru
>>>>> <mailto:alexxy at omrb.pnpi.spb.ru>>wrote:
>>>>>
>>>>> Hi all!
>>>>>
>>>>> Its good idea to drop deprecated force fields!
>>>>>
>>>>> BTW are there any plans to add some new forcefields from
>>>>> contributuions pages?
>>>>>
>>>>> Peter Kasson ????? 14-02-2014 18:47:
>>>>>
>>>>> Sounds good to me! If anyone has a burning need to use
>>>>> them, they
>>>>> can still of course do so, but having them part of the
>>>>> supported
>>>>> distribution doesn't seem like a good idea at this point.
>>>>>
>>>>> --Peter
>>>>>
>>>>> ----------------------------------------------------------------------
>>>>> Peter Kasson, MD, PhD
>>>>> Assistant Professor
>>>>> Departments of Molecular Physiology and Biological Physics
>>>>> and of Biomedical Engineering
>>>>> University of Virginia
>>>>>
>>>>> On Fri, Feb 14, 2014 at 6:39 AM, Erik Lindahl
>>>>> <erik.lindahl at scilifelab.se
>>>>> <mailto:erik.lindahl at scilifelab.se>> wrote:
>>>>>
>>>>> Agreed!
>>>>>
>>>>> On 14 Feb 2014, at 06:37, Rossen Apostolov
>>>>> <rossen at kth.se <mailto:rossen at kth.se>> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> Encad and GmxFF have been deprecated for a while.
>>>>> Now before 5.0
>>>>>
>>>>> is a good time for cleanup, if nobody is using them.
>>>>>
>>>>>
>>>>> Any objections?
>>>>>
>>>>> Rossen
>>>>> _______________________________________________
>>>>> Gromacs Core Developers mailing list
>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-core
>>>>>
>>>>> [1]
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Gromacs Core Developers mailing list
>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-core
>>>>> [1]
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Links:
>>>>> ------
>>>>> [1]https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-core
>>>>>
>>>>>
>>>>> --
>>>>> 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:alexxyum at gmail.com>
>>>>> mailto:alexxy at gentoo.org <mailto:alexxy at gentoo.org>
>>>>> mailto:alexxy at omrb.pnpi.spb.ru <mailto:alexxy at omrb.pnpi.spb.ru>
>>>>>
>>>>> --
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>>>>>
>>>>>
>>>>>
>>>>
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>>>
>>
>> --
>> Dr Thomas Piggot
>> University of Southampton, UK.
>> --
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>
>
>
--
Dr Thomas Piggot
University of Southampton, UK.
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