Idea Paper : Development of a Software Framework for Formalizing Forcefield Atom-Typing for Molecular Simulation

Forcefields are a crucial ingredient of Molecular Dynamics (MD) simulations, describing the types and parameters of interactions between the simulated particles. These parameter sets, however, are typically specific to the molecule in which the atoms appears, where within the molecule the atom is positioned, the phase or state point of the system, as well as the simulator tool in use. This makes choosing the correct parameter values a tedious and error prone task. Forcefield parameters, furthermore, are often hard to locate: some are published in scientific papers, others come with MD tools, often with no or ambiguous documentation on their applicability. In this paper, we present a framework that aims to solve this data management issue, proposing a common format for forcefields that is self-documenting with machine readable, declarative usage rules. We believe that processes and tools that are commonly used today in software development (e.g, unit testing, verification and validation, continuous integration, and version control) are, with proper infrastructure support, applicable to forcefield development, as well. The paper describes how such an infrastructure can tackle managing and evolving forcefields by the MD community, and proposes a way to encourage and incentivize involvement by the stakeholders.