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

[Alexey Shvetsov]

Mark Abraham писал 14-02-2014 20:12:
> Removing encad and gmx sounds good. Probably don't have time to rip
> out the code that supported encad.
> 
> 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?

AFAIK there are few good candidates from this page

amber99sb_parmbsc0 - i use it for medelling of different nucleosome 
assembly/disassembly states
charmm36
  and may bi others

I have some (unfinished) attempts to port glycam forcefield to gromacs 
(i use some parts of it to model highly glycosilated protein)

> 
> 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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-- 
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