This option is even better ...
Ray
On Thu, Apr 28, 2011 at 1:11 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Thursday, April 28, 2011, Carlos Simmerling
> <carlos.simmerling.gmail.com> wrote:
>> this makes good sense, but we don't want them to think that for example ff11
>> and ff11pol are similar except the pol being added in. sort of suggests that
>
> Why not reserve ff for additive models, ua for united atom, and pol
> for polarizable; ff11, ua11, and pol11. This makes them seem less like
> one another but still retains the simplicity of Tom's suggestion.
>
> -Dan
>
>> just the year alone isn't really enough to describe it. maybe for short
>> labels it doesn't matter, and there can be a table that describes what goes
>> into each ffxx (charge model, etc)
>> On Thu, Apr 28, 2011 at 3:58 PM, Thomas Cheatham III <tec3.utah.edu> wrote:
>>
>>>
>>> > we should have a discussion about force field parameter set names. I've
>>> been
>>> > told that "parm11" is the planned name for the new polarizable force
>>> field.
>>> > We had planned ff11 to be the new additive model. None of these are
>>> really
>>>
>>> "parm" is outdated as we all agreed when we moved to the ff convention.
>>> I also think that DAC has led-- in consultation with the developers-- the
>>> naming choices. So despite what someone publishes and refers to in their
>>> paper as the name, how it gets referred to in AMBER has been set by the
>>> developers.
>>>
>>> My personal opinion is that the "default", best tested, and most widely
>>> and routinely applied should be ffXX and arguably, these are the additive
>>> models. For the united atom, we add ua. Perhaps for the polarizable, we
>>> should add pol...
>>>
>>> ff11ua - united atom
>>> ff11 - additive
>>> ff11pol - polarizable
>>>
>>> [Of course, we could call the new additive one ff12 and confuse things
>>> further with ff11 polarizable and ff12 not but "newer".]
>>>
>>> We almost need a three tiered naming:
>>>
>>> ffXX-model-group
>>>
>>> model: additive = "", ua, pol, ...
>>>
>>> group: AMBER = "", ildn, sb, shaw, best, ...
>>>
>>> If AMBER sanctioned then no group specification is provided. If additive,
>>> no model specification is provided.
>>>
>>> --tom
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER-Developers mailing list
>>> AMBER-Developers.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>>
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Thu Apr 28 2011 - 15:00:03 PDT
