Wan, S;
Sinclair, RC;
Coveney, PV;
(2021)
Uncertainty quantification in classical molecular dynamics.
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences
, 379
(2197)
, Article 20200082. 10.1098/rsta.2020.0082.
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Abstract
Molecular dynamics simulation is now a widespread approach for understanding complex systems on the atomistic scale. It finds applications from physics and chemistry to engineering, life and medical science. In the last decade, the approach has begun to advance from being a computer-based means of rationalizing experimental observations to producing apparently credible predictions for a number of real-world applications within industrial sectors such as advanced materials and drug discovery. However, key aspects concerning the reproducibility of the method have not kept pace with the speed of its uptake in the scientific community. Here, we present a discussion of uncertainty quantification for molecular dynamics simulation designed to endow the method with better error estimates that will enable it to be used to report actionable results. The approach adopted is a standard one in the field of uncertainty quantification, namely using ensemble methods, in which a sufficiently large number of replicas are run concurrently, from which reliable statistics can be extracted. Indeed, because molecular dynamics is intrinsically chaotic, the need to use ensemble methods is fundamental and holds regardless of the duration of the simulations performed. We discuss the approach and illustrate it in a range of applications from materials science to ligand-protein binding free energy estimation. This article is part of the theme issue 'Reliability and reproducibility in computational science: implementing verification, validation and uncertainty quantification in silico'.
| Type: | Article |
|---|---|
| Title: | Uncertainty quantification in classical molecular dynamics |
| Location: | England |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1098/rsta.2020.0082 |
| Publisher version: | https://doi.org/10.1098/rsta.2020.0082 |
| Language: | English |
| Additional information: | © 2021 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/). |
| Keywords: | free energy calculation, molecular dynamics simulation, uncertainty quantification |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > UCL BEAMS UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences > Dept of Chemistry |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10125525 |
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