> 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"parm" is outdated as we all agreed when we moved to the ff convention.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 - 13:00:04 PDT
