Good evening, I have been communicating with Suresh and Marlon about creating a gateway for Molecular Dynamics (MD) simulation and analysis software, specifically the OpenMM software package (http://openmm.org/) and the MDTraj analysis framework (http://mdtraj.org). MD studies typically require hundreds to thousands of independent simulations distributed over a cluster to gather sufficient data, with simulations running for days, weeks, months, or longer, depending on the size of the molecule. Because of these considerations, tools are needed for creating and distributing simulations, monitoring simulations as they run, and performing certain actions as events occur during simulation.
The goal of this project is to extend Apache Airavata in the following ways: - monitoring running simulations for user-defined events - performing user-defined actions when an event occurs - monitoring system resources - streaming partial simulation results and system resource usage I have previously collaborated on a piece of software called Folding@Work (named for Folding@Home <https://folding.stanford.edu/home/>), which distributes simulations and returns partial results for analysis, which could serve as a prototype for the functionality described above. This project is being considered as a Google Summer of Code proposal, and I would appreciate any comments or suggestions to improve these ideas. Best, Jeff Kinnison
