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

Berk Hess hess at kth.se
Fri Feb 14 17:24:57 CET 2014

On 02/14/2014 05:16 PM, Justin Lemkul wrote:
> On 2/14/14, 11:12 AM, Mark Abraham wrote:
>> 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?
>> 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?
> Yes, we're working on that.  I'm personally looking into the best ways 
> to run CHARMM force fields within Gromacs.  Couple that with my 
> ongoing implementation of our Drude algorithms and I think 5.1 is a 
> good target.  Our only reservations about including a CHARMM36 force 
> field directory in Gromacs are: (1) we update the force field quite 
> frequently, certainly more often than Gromacs versions are released 
> and (2) we keep detailed statistics about downloads from our lab 
> website to help track usage (and get grants :).
> At minimum, I am perfectly happy to oversee the coordination between 
> Gromacs and the CHARMM force fields in terms of making sure we have a 
> suitable (recent) distribution ready whenever a new Gromacs release 
> comes out.
Maybe (but maybe not) we currently need a little extra functionality in 
Gromacs for CHARMM36. But after that, the force-field files should be 
independent of the Gromacs version. Force-field distributions not 
included into the Gromacs distribution can be updated independently from 
the code/releases.

Are parameters of existing common molecules being updated in CHARMM36, 
or are only new molecules being added?


> -Justin

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