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From Jeffery Kinnison <>
Subject GSoC Proposal: In-Situ Molecular Dynamics Data Analysis
Date Sat, 19 Mar 2016 22:38:03 GMT
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 ( and the MDTraj analysis
framework ( 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 <>), 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.

Jeff Kinnison

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