AMBER Archive (2006)

Subject: RE: AMBER: ab initio terminology query

From: Yong Duan (
Date: Wed Nov 01 2006 - 12:53:39 CST

Just chip-in my 2 cents ...

Ross made a number of excellent points. But I do not think Jiri quite meant
what Ross thought he meant :).

As for optimization, although the accepted approach, following the tradition
of Cornell et al, is to use relatively in-expensive (in today's scale)
optimization. Don't forget, Cornall et al's paper was published in last
millennium when HF/6-31G* was considered an expensive and accurate model. In
today's standard, it is just a model. As for peptide chemistry, I am not
convinced that we should be bound by this limitation which was more or less
due to the speed (or lack of it) of supercomputers in last century. If we
also use the term "supercomputer" as the "moving" standard, we might be more
inclined to think beyond what was available a decade ago.

However, if the purpose is to calculate the electrostatic potential to fit
the charges, the "conventional wisdom" thinks optimizations do not have to
be as thorough. Having said that, it is still a matter of unsettled issue as
to how and how much that subtle differences in charge distribution would
affect the property besides the obvious dipoles and other-poles. Not to
drive this discussion awfully off the track, molecular properties, as for
peptide-chemistry in solvent, are probably more influenced by local
chemistry than long-range field. In other words, the influence of charge
distribution to the 1-4 energy, which is intricately related to the torsion
energy (as a matter of fact should be considered part of it), is probably
more important.


> With regards to the
> optimisation part
> of the calculation I think one could discuss this for ever.

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