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On The Importance of Accurate Algorithms for Reliable Molecular Dynamics Simulations

preprint
submitted on 30.12.2019 and posted on 31.12.2019 by Berk Hess, David van der Spoel, Mark J. Abraham, Erik Lindahl

Molecular dynamics is expected to produce accurate results over a wide range of conditions and timescales. However, this is not always the case since the field has been too reluctant to abandon historically popular techniques known to introduce artefacts. Two recent papers have suggested there are reliability issues in the GROMACS code since it no longer uses a legacy twin-range algorithm. Here, we show there are order-of-magnitude differences in accuracy favoring the modern Trotter decomposition, and that a force field relying on the old algorithm will have errors parametrized into the force field. Similarly, the suggestions about incorrect virial calculations turn out to be explained by insufficient accuracy in the default SHAKE settings used for GROMOS, while the GROMACS default choices are accurate. This highlights the importance of being more critical to error cancellation in simulations in order for algorithms and parameters to both gradually converge to more perfect ones.

Funding

Vetenskapsrådet

BioExcel-2 Centre of Excellence for Computational Biomolecular Research

European Commission

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SNIC 2.0: Swedish National Infrastructure for Computing

Swedish Research Council

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History

Email Address of Submitting Author

erik@kth.se

Institution

KTH Royal Institute of Technology

Country

Sweden

ORCID For Submitting Author

0000-0002-2734-2794

Declaration of Conflict of Interest

N/A

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