Formalizing Atom-typing and the Dissemination of Force Fields with Foyer

A key component to enhancing reproducibility in the molecular simulation community is reducing ambiguity in the parameterization of molecular models. Ambiguity in molecular models often stems from the dissemination of molecular force fields in a format that is not directly usable or is ambiguously documented via a non-machine readable mechanism. Specifically, the lack of a general tool for performing automated atom-typing under the rules of a particular force field facilitates errors in model parameterization that may go unnoticed if other researchers are unable reproduce this process. Here, we present Foyer, a Python tool that enables users to define force field atom-typing rules in a format that is both machine- and human-readable thus eliminating ambiguity in atom-typing and additionally providing a framework for force field dissemination. Foyer defines force fields in an XML format, where SMARTS strings are used to define the chemical context of a particular atom type. Herein we describe the underlying methodology of the Foyer package, highlighting its advantages over typical atom-typing approaches and demonstrate is application in several use-cases.Comment: 39 Page, 4 Figures, 8 Listing

SI2-SSE: Development of a Software Framework for Formalizing ForceField Atom-Typing for Molecular Simulation

<p>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. </p

Radio interferometric tracking of mobile wireless nodes

Location-awareness is an important requirement for many mobile wireless applications today. When GPS is not applicable because of the required precision and/or the resource constraints on the hardware platform, radio interferometric ranging may offer an alternative. In this paper, we present a technique that enables the precise tracking of multiple wireless nodes simultaneously. It relies on multiple infrastructure nodes deployed at known locations measuring the position of tracked mobile nodes using radio interferometry. In addition to location information, the approach also provides node velocity estimates by measuring the Doppler shift of the interference signal. The performance of the technique is evaluated using a prototype implementation on mote-class wireless sensor nodes. Finally, a possible application scenario of dirty bomb detection in a football stadium is briefly described

SI2-SSE: Development of a Software Framework for Formalizing ForceField Atom-Typing for Molecular Simulation

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