[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
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>>>>>             [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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