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
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 "parm" is outdated as we all agreed when we moved to the ff convention.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
Received on Thu Apr 28 2011 - 13:30:02 PDT
