Free Energy Landscape Analysis System Based on Parallel Molecular Dynamics Simulation

Masakazu Sekijima; Jun Doi; Shinya Honda; Tamotsu Noguchi; Shigenori Shimizu; Yutaka Akiyama

doi:10.2197/ipsjdc.3.757

Masakazu Sekijima, Jun Doi, Shinya Honda, Tamotsu Noguchi, Shigenori Shimizu, Yutaka Akiyama

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JOURNAL FREE ACCESS

2007 Volume 3 Pages 757-766

DOI https://doi.org/10.2197/ipsjdc.3.757

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Abstract

We created a Free Energy Landscape Analysis System based on a parallelized molecular dynamics (MD) simulation adapted for the IBM Blue Gene/L supercomputer. We begin with an outline of our Free Energy Landscape Analysis system. Next we discuss how Parallel MD was tuned for Blue Gene/L. We then show the results for some test targets run on Blue Gene/L, including their efficiency. Finally, we mention some future directions for extension of this project.

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