This convention has been used and is a good one. Let's stay with it ...
Ray
On Thu, Apr 28, 2011 at 12:58 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 "parm" is outdated as we all agreed when we moved to the ff convention.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 - 15:00:03 PDT
