I agree with your assessment--OPLS predates the modern Amber methods. I've
never spoken with Wendy, but perhaps I should sometime.
On Mar 11, 2016 7:52 PM, "Thomas Cheatham" <tec3.utah.edu> wrote:
>
> > myself. What I can tell you for the moment is that OPLS, in fact a
> > historical derivative of Amber which has long since grown into its own
>
> A minor point of clarification, and DAC or Merz can correct me if I am
> wrong, but I think AMBER adopted the OPLS approach, not the other way
> around. The key here is not the intramolecular (which were similar or
> shared in both cases), but the intermolecular terms and the use of liquid
> phase simulations to fit vdw parameters to reproduce density. The
> approaches started to differentiate when AMBER realized the electrostatic
> potential charge fitting for the charges (as opposed to empirical charge
> or QM-interaction energy charge fitting which occured prior to the OPLS
> liquid density matching ideas) was a potentially better, but not
> sufficient approach. They needed balance and hence adopted the OPLS idea
> of vdw from neat liquid simulations. From the classic 1995 Cornell et al.
> parm94 paper: "We have been influenced by the OPLS philosophy of balanced
> solvent-solvent and solute-solvent interactions in our thoughts about a
> second-generation force field..."
>
> As an aside, it is interesting to go back to Jorgenson's 1988 article
> where quotes like the following appear: "Computer simulations are
> undoubtedly destined to become an increasingly important means for
> investigating the structures and dynamics of biological systems" and
> "There is little doubt that there will be a continual evolution in force
> fields with added complexity and improved performance". Wow! So much has
> improved *yet*, so much has stayed the same.
>
> I am reinvigorated reading these papers again. Those of you new to the
> field and/or those who *haven't* read the earlier papers should take the
> time to read and understand these earlier force field papers... This is a
> better use of time than blindly applying MM-GBSA calculations.
>
> --tec3
>
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Received on Sat Mar 12 2016 - 16:30:03 PST
