[gmx-developers] [gmx-core] removal of encad and gmx FF in 5.0?

[Erik Lindahl]

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> 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> 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 писал 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> wrote:
>> 
>> Agreed!
>> 
>> On 14 Feb 2014, at 06:37, Rossen Apostolov <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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>> -- 
>> 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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