Comment by dekhn | Hacker News Reader

Comment by dekhn | Hacker News Reader

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When I say ab initio I mean "classical newtonian force field with approximate classical terms derived from QM", AKA something like https://ambermd.org/AmberModels.php

Other people use ab initio very differently (for example, since you said "level of theory" I think you mean basis set). I don't think something like QM levels of theory provide a great deal of value on top of classical (and at a significant computational cost), but I do like 6-31g* as a simple set.

Other people use ab initio very differently. For example, CASP, the protein structure prediction, uses ab initio very loosely to me: "some level of classicial force field, not using any explicit constraints derived from homology or fragment similarity" which typically involves a really simplified or parameterized function (ROSETTA).

Personally I don't think atomistic simulations of cells really provide a lot of extra value for the detail. I would isntead treat cell objects as centroids with mass and "agent properties" ("sticks to this other type of protein for ~1 microsecond"). A single ribosome is a single entity, even if in reality it's made up of 100 proteins and RNAs, and the cell membrane is modelled as a stretchy sheet enclosing an incompressible liquid.

Level of theory as it relates to an-initio QM calculations usually indicates Hartee Fock, MP2 and so on, then the basis set gets specified after.

I also agree that QM doesn't provide much for the cost at this scale, I just wish the term ab initio would be left to QM folks, as everything else is largely just the parameterization you mentioned.

The systemn I work with, AMBER, explains how individual classical terms are derived: https://ambermd.org/tutorials/advanced/tutorial1/section1.ht... which appears te be MP2/6-31g* (sorry, I never delved deeply into the QM parts). Once those terms are derived, along with various approximated charges (classical fields usually just treat any charge as point-centered on the nucleus, which isn't great for stuff like polarizable bonds), everything is purely classical springs and dihedrals and interatomic potentials based on distance.

I am more than happy to use "ab initio" purely for QM, but unfortunately the term is used widely in protein folding and structure prediction. I've talked exdtensively with David Baker and John Moulton to get them to stop, but they won't.

I would not describe AMBER, or anything using a newtonian force field, as ab initio.

In inorganic materials ab initio means you actually solve Schrodinger's equation (though obviously with aggressive simplifications e.g. Hartree-Fock).

Sure. But in the protein structure prediction field, "ab initio" is used to mean "structure was predicted with no homology or other similarity information" even though the force fields incorporate an enormous amount of protein structural knowledge.

I guess it's just wierd to me to see ab initio used to describe a class of methods than in my field it explicitly precludes.

Having developed a few newtonian force fields, calling them "derived from QM" is very, very generous :P

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