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  On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size

Gapsys, V., & de Groot, B. L. (2020). On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size. eLife, 9: e57589. doi:10.7554/eLife.57589.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0007-0807-9 Version Permalink: http://hdl.handle.net/21.11116/0000-0007-080A-6
Genre: Journal Article

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Gapsys, V.1, Author              
de Groot, B. L.1, Author              
Affiliations:
1Research Group of Computational Biomolecular Dynamics, MPI for biophysical chemistry, Max Planck Society, ou_578573              

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Free keywords: Tools and Resources; Structural Biology and Molecular Biophysics; Molecular Dynamics; Simulation; Statistics; Thermodynamics; Kinetics
 Abstract: Computational simulations, akin to wetlab experimentation, are subject to statistical fluctuations. Assessing the magnitude of these fluctuations, that is, assigning uncertainties to the computed results, is of critical importance to drawing statistically reliable conclusions. Here, we use a simulation box size as an independent variable, to demonstrate how crucial it is to gather sufficient amounts of data before drawing any conclusions about the potential thermodynamic and kinetic effects. In various systems, ranging from solvation free energies to protein conformational transition rates, we showcase how the proposed simulation box size effect disappears with increased sampling. This indicates that, if at all, the simulation box size only minimally affects both the thermodynamics and kinetics of the type of biomolecular systems presented in this work.

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Language(s): eng - English
 Dates: 2020-09-09
 Publication Status: Published online
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 Rev. Type: Peer
 Identifiers: DOI: 10.7554/eLife.57589
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Title: eLife
Source Genre: Journal
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Pages: - Volume / Issue: 9 Sequence Number: e57589 Start / End Page: - Identifier: -