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MDBenchmark: A Toolkit to Optimize the Performance of Molecular Dynamics Simulations

preprint
revised on 27.08.2020 and posted on 28.08.2020 by Michael Gecht, Marc Siggel, Max Linke, Gerhard Hummer, Juergen Koefinger
Molecular dynamics simulations resolve biomolecular processes and material properties with incomparable detail. As a result, they consume a significant fraction of worldwide supercomputing resources. With our open source benchmarking software MDBenchmark, expert and novice users alike can easily determine the optimal settings for their specific simulation system, MD engine, software environment, and hardware configuration. Ultimately, saving computation time, energy, and money at essentially no additional cost will produce better science.

Funding

Max Planck Society

Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz (LOEWE) DynaMem program of the state of Hesse

History

Email Address of Submitting Author

juergen.koefinger@biophys.mpg.de

Institution

Max Planck Institute of Biophysics

Country

Germany

ORCID For Submitting Author

0000-0001-8367-1077

Declaration of Conflict of Interest

We declare no conflict of interest.

Version Notes

The article has been submitted to The Journal of Chemcial Physics. After it is published, it will be found at https://aip.scitation.org/journal/jcp.

Exports