SI2-SSE: Development of a Software Framework for Formalizing ForceField Atom-Typing for Molecular Simulation
2018-04-23T20:22:03Z (GMT) by
The availability of forcefields for molecular simulation has reduced the effort researchers must devote to the difficult and costly task of determining the interactions between species, allowing them to instead focus on the motivating scientific questions. However, determining which parameters in a forcefield to use is still often a tedious and error prone task. Forcefields can contain tens or hundreds of different types of the same element, where each type represents the element in a different chemical context. The documentation of a typical forcefield tends to be scarce and unstructured, commonly expressed in plain text or in an ad-hoc shorthand notation, leading to ambiguities and increasing the likelihood of incorrect usage. While there are freely available tools to aid in atom-typing, these are typically specific to a particular forcefield or simulator and capture the atom-typing and parameterization rules in ways that are hard to maintain, debug, and evolve. This work proposes to establish a formalism to express the chemical context for which a particular forcefield parameter is applicable (i.e., forcefield usage semantics) and an atom-typing tool that interprets this formalism to generate forcefield parameterizations that are provably correct.