Molecular Modeling: Molecular Mechanics. C372 Introduction to Cheminformatics II Kelsey Forsythe. Guidelines for Use. What systems were used to parameterize How is energy calculated What assumptions are used in the force field How has it performed in the past. Transferability.
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Molecular Modeling:Molecular Mechanics
Introduction to Cheminformatics II
0 at minimum
H2 in Pd
Christensen, O. B. et. al, Phys. Rev. B. 40, 1993 (1989)
Van derWaals repulsion
The form for the repulsive part has no physical basis and is for computational convenience when working with largemacromolecules. K. Gilbert: Force fields like MM2 which is used for smaller organic systems will use a Buckingham potential (or expontential) which accurately reflects the
N >> 1000 atoms
Not robust enough to describe subtle chemical effects
Does not reproduce quantal nature