[gmx-developers] [gmx-core] removal of encad and gmx FF in 5.0?
Thomas Piggot
t.piggot at soton.ac.uk
Mon Feb 17 20:35:26 CET 2014
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
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>>>
>>>
>>> Links:
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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: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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