377 Software Engineering in and for the Molecular Sciences

Tuesday, November 15, 2016: 12:30 PM - 3:00 PM
Yosemite A (Hilton San Francisco Union Square)
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:
Frank T. Willmore
Email: Frank.Willmore@HDFGroup.org

Co-chairs:
Coray M. Colina
Email: colina@chem.ufl.edu

Eric Jankowski
Email: ericjankowski@boisestate.edu


12:30 PM
(377a) Best Practices in Collaborative Software Development: Lessons Learned in the Rosetta Commons
Jeffrey Gray

12:55 PM
(377b) Validation of Computational Models and Codes
Christopher R. Iacovella, Christoph Klein, János Sallai and Ahmed E. Ismail

1:20 PM
(377c) Pysimm: A Python Package for Simulation of Amorphous Polymeric System
Michael E. Fortunato and Coray M. Colina

1:32 PM
(377d) Automated Event Detection and Rate Constants for Complex Systems with Reaxff
N. Ole Carstensen, Malte Döntgen and Kai Leonhard

1:44 PM
(377e) Freud: A Software Suite for High-Throughput Simulation Analysis
Eric S. Harper, Matthew Spellings, Joshua A. Anderson and Sharon C. Glotzer

1:56 PM
(377f) PB-[S]AM, a Novel Solution to the Poisson-Boltzmann Equation for Applications Ranging from Protein Simulations to Polymer Membrane Design
Lisa Felberg, Marielle Soniat, David Brookes, Enghui Yap and Teresa Head-Gordon

2:08 PM
(377g) Multi-GPU Electrostatics and Rigid Bodies in HOOMD-Blue 2.0
Jens Glaser, Joshua A. Anderson and Sharon C. Glotzer

2:20 PM
(377h) Scientific Data Management with Signac
Paul Dodd, Carl Simon Adorf and Sharon C. Glotzer

2:32 PM
(377i) Automated Molecular Modeling Via Optimization of Force Field Parameters
Andreas Krämer, Marco Hülsmann, Karl N. Kirschner and Dirk Reith

2:44 PM
(377j) Efficient Neighbor List Calculation for Molecular Simulation of Colloidal Systems Using Graphics Processing Units
Michael P. Howard, Joshua A. Anderson, Arash Nikoubashman, Sharon C. Glotzer and Athanassios Z. Panagiotopoulos
See more of this Group/Topical: Computational Molecular Science and Engineering Forum
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