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

Jankowski, E., Boise State University

Co-Chairs

Colina, C., University of Florida
Willmore, F. T., National Institute of Standards and Technology

Presentations

12:30 PM

(736a) Automated Tests for Physical Validity in Molecular Dynamics and Monte Carlo Simulations
Shirts, M., Merz, P.

12:44 PM

(736b) Recent Developments in the HOOMD Simulation Ecosystem
Glotzer, S. C., Glaser, J., Anderson, J. A.

01:04 PM

(736c) Using Graphs to Quantify Energetic and Structural (dis)Order in Organic Thin Films
Wodo, O., Jankowski, E., Jones, M., Hiller, A., Van, E.

01:18 PM

(736d) Interactive Extensible Molecular Simulations with Etomica
Schultz, A., Kofke, A. D., Kofke, D.

01:38 PM

(736e) A General Algorithm for Efficient Reverse-Mapping of Coarse-Grained Configurations to the Atomistic Scale
Nowak, C., Escobedo, F., Misra, M.

01:52 PM

(736f) Mosdef: Molecular Simulation and Design Framework
Klein, C., Sallai, J., Summers, A. Z., Iacovella, C., Lédeczi, Á., McCabe, C., Cummings, P.

02:12 PM

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

02:26 PM

(736h) Foyer: A Framework for Defining Force Field Usage Semantics and Atom-Typing Molecular Systems
Klein, C., Sallai, J., Summers, A. Z., Cummings, P., Iacovella, C., McCabe, C.

02:46 PM

(736i) Using the k-d Tree Data Structure to Accelerate Monte Carlo Simulations
Chen, Q., Xue, B., Siepmann, J.