Dear All,
If that's the case, then can one think of a tolerance limit for the range
of expected "good" parameter values such that outside this range the
simulation is most likely going to be wrong.
In my small experience, Amber/AmberTools doesn't warn about the wrong set
of parameters and runs as long as it gets some value for each expected
parameter.
Wouldn't it be better to first check for such tolerances, if they exist
(I'm guessing that they should), and warn the user that your parameters are
probably wrong or not within tolerance limits?
Thank you and best regards.
On Mon, Apr 5, 2021 at 9:02 PM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> yes I also remember Peter saying that, and also saying often that you
> needed to fix the biggest problems first, eg no point to bond anharmonicity
> if you don't have good charges, etc.
> no I don't know of a paper, but he did write a couple ff reviews IIRC.
> carlos
>
> On Mon, Apr 5, 2021 at 11:12 AM Brent Krueger <kruegerb.hope.edu> wrote:
>
> > Hey AMBER listers,
> >
> > With regard to force-field parameters, I can remember Peter Kollman often
> > saying that maintaining balance among all of the parameters was far more
> > important than the accuracy of any single parameter.
> >
> > Two questions about this for the crowd:
> > a) Is that also what others recall, or am I remembering that wrong?
> >
> > b) Is anyone aware whether that was evaluated or at least written down
> in a
> > paper somewhere that can be referenced? And I realize that there are
> > 10,000 MD papers that mention the need to walk the line between accuracy
> > vs. transferability in force fields in a general way. That's not what I
> > mean here. I mean something a bit more specific with regard to a
> > philosophy that undergirds all of the Cornell-type force fields.
> >
> > Thanks,
> > Brent
> >
> > --
> > _______________________________________________
> > Brent P. Krueger (he/him/his)......phone: 616 395 7629
> > Professor......................................fax: 616 395 7118
> > Hope College...............................Schaap Hall 2120
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> > Holland, MI 49423
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--
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Received on Mon Apr 05 2021 - 09:30:02 PDT
