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

revised on 27.08.2020, 15:58 and posted on 28.08.2020, 08:11 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.


Max Planck Society

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


Email Address of Submitting Author


Max Planck Institute of Biophysics



ORCID For Submitting Author


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