736 Software Engineering in and for the Molecular Sciences


Description:
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.

Sponsor:
Computational Molecular Science and Engineering Forum


Chair:
Eric Jankowski
Assistant Professor
Boise State University
Micron School of Materials
Boise, ID
80207
Email: ericjankowski@boisestate.edu

Co-chairs:
Coray M. Colina
Professor
University of Florida
Chemistry
121 Steidle Building
Gainesville, FL
16802
Fax Number: 814-865-2917
Email: colina@chem.ufl.edu

Frank T. Willmore
Software Engineer
The HDF Group
Mail Code R8700
Champaign, IL
78712
Email: Frank.Willmore@HDFGroup.org


Papers:
736a
Automated Tests for Physical Validity in Molecular Dynamics and Monte Carlo Simulations
Pascal Merz, University of Colorado Boulder; Michael Shirts, University of Colorado Boulder
736b
Recent Developments in the HOOMD Simulation Ecosystem
Sharon C. Glotzer, University of Michigan; Jens Glaser, University of Michigan; Joshua A. Anderson, University of Michigan
736c
Using Graphs to Quantify Energetic and Structural (dis)Order in Organic Thin Films
Alexander Hiller, University at Buffalo; Ellen Van, University at Buffalo; Matthew Jones, Boise State University; Eric Jankowski, Boise State University; Olga Wodo, SUNY Buffalo
736d
Interactive Extensible Molecular Simulations with Etomica
Andrew J. Schultz, University at Buffalo, The State University of New York; Alexander D. Kofke, University at Buffalo; David A. Kofke, University at Buffalo, The State University of New York
736e
A General Algorithm for Efficient Reverse-Mapping of Coarse-Grained Configurations to the Atomistic Scale
Christian Nowak, Cornell University; Mayank Misra, Cornell University; Fernando Escobedo, Cornell University
736f
Mosdef: Molecular Simulation and Design Framework
Christoph Klein, Vanderbilt University; János Sallai, Vanderbilt University; Andrew Z. Summers, Vanderbilt University; Christopher R. Iacovella, Vanderbilt University; Ákos Lédeczi, Vanderbilt University; Clare McCabe, Vanderbilt University; Peter T. Cummings, Vanderbilt University
736g
Massively-Parallel Mesoscale Hydrodynamics on Graphics Processing Units
Michael P. Howard, Princeton University; Athanassios Z. Panagiotopoulos, Princeton University; Arash Nikoubashman, Johannes Gutenberg University Mainz
736h
Foyer: A Framework for Defining Force Field Usage Semantics and Atom-Typing Molecular Systems
Christoph Klein, Vanderbilt University; Andrew Z. Summers, Vanderbilt University; Peter T. Cummings, Vanderbilt University; János Sallai, Vanderbilt University; Christopher R. Iacovella, Vanderbilt University; Clare McCabe, Vanderbilt University
736i
Using the k-d Tree Data Structure to Accelerate Monte Carlo Simulations
Qile Chen, University of Minnesota; Bai Xue, University of Minnesota; J. Ilja Siepmann, University of Minnesota
Abstract Submissions Closed
See more of this Group/Topical: Computational Molecular Science and Engineering Forum
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