2017 Annual Meeting

Session: Software Engineering in and for the Molecular Sciences

This session presents contributions to molecular sciences with a focus on software development. Submissions including new trajectory analysis tools, advanced sampling techniques, image processing, plugins to established packages such as LAMMPS, HOOMD, NAMD, VMD, AMBER, etc, and work improving the software and compiler stacks which support molecular simulation are encouraged.

Chair

Eric Jankowski, Boise State University

Co-Chairs

Coray Colina, University of Florida
Frank T. Willmore, National Institute of Standards and Technology

Presentations

12:30 PM

(736a) Automated Tests for Physical Validity in Molecular Dynamics and Monte Carlo Simulations
Michael Shirts, Pascal Merz

12:44 PM

(736b) Recent Developments in the HOOMD Simulation Ecosystem
Sharon C. Glotzer, Jens Glaser, Joshua A. Anderson

01:04 PM

(736c) Using Graphs to Quantify Energetic and Structural (dis)Order in Organic Thin Films
Olga Wodo, Eric Jankowski, Matthew Jones, Alexander Hiller, Ellen Van

01:18 PM

(736d) Interactive Extensible Molecular Simulations with Etomica
Andrew Schultz, Alexander D. Kofke, David Kofke

01:38 PM

(736e) A General Algorithm for Efficient Reverse-Mapping of Coarse-Grained Configurations to the Atomistic Scale
Christian Nowak, Fernando Escobedo, Mayank Misra

01:52 PM

(736f) Mosdef: Molecular Simulation and Design Framework
Christoph Klein, János Sallai, Andrew Z. Summers, Christopher Iacovella, Ákos Lédeczi, Clare McCabe, Peter Cummings

02:12 PM

(736g) Massively-Parallel Mesoscale Hydrodynamics on Graphics Processing Units
Michael P. Howard, Athanassios Z. Panagiotopoulos, Arash Nikoubashman

02:26 PM

(736h) Foyer: A Framework for Defining Force Field Usage Semantics and Atom-Typing Molecular Systems
Christoph Klein, János Sallai, Andrew Z. Summers, Peter Cummings, Christopher Iacovella, Clare McCabe

02:46 PM

(736i) Using the k-d Tree Data Structure to Accelerate Monte Carlo Simulations
Qile Chen, Bai Xue, Joern Siepmann