Escaping Atom Types in Force Fields Using Direct Chemical Perception.

ABSTRACT: Traditional approaches to specifying a molecular mechanics force field encode all the information needed to assign force field parameters to a given molecule into a discrete set of atom types. This is equivalent to a representation consisting of a molecular graph comprising a set of vertices, which represent atoms labeled by atom type, and unlabeled edges, which represent chemical bonds. Bond stretch, angle bend, and dihedral parameters are then assigned by looking up bonded pairs, triplets, and quartets of atom types in parameter tables to assign valence terms and using the atom types themselves to assign nonbonded parameters. This approach, which we call indirect chemical perception because it operates on the intermediate graph of atom-typed nodes, creates a number of technical problems.

SUBMITTER: Mobley DL 

PROVIDER: S-EPMC6245550 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature