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 "parm" is outdated as we all agreed when we moved to the ff convention.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
>>
>>
>>
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Received on Thu Apr 28 2011 - 13:30:03 PDT
