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

Authors
  • Gapsys, Vytautas1
  • de Groot, Bert L1
  • 1 Computational Biomolecular Dynamics Group, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany. , (Germany)
Type
Published Article
Journal
eLife
Publisher
"eLife Sciences Organisation, Ltd."
Publication Date
Aug 19, 2020
Volume
9
Identifiers
DOI: 10.7554/eLife.57589
PMID: 32812868
Source
Medline
Keywords
Language
English
License
Unknown

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. © 2020, Gapsys and de Groot.

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