On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size
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 simulat...
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doaj-47da752ef6744562a861e0f25d852add2021-05-05T21:25:39ZengeLife Sciences Publications LtdeLife2050-084X2020-08-01910.7554/eLife.57589On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box sizeVytautas Gapsys0https://orcid.org/0000-0002-6761-7780Bert L de Groot1https://orcid.org/0000-0003-3570-3534Computational Biomolecular Dynamics Group, Max-Planck Institute for Biophysical Chemistry, Göttingen, GermanyComputational Biomolecular Dynamics Group, Max-Planck Institute for Biophysical Chemistry, Göttingen, GermanyComputational 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.https://elifesciences.org/articles/57589molecular dynamicssimulationstatisticsthermodynamicskinetics |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Vytautas Gapsys Bert L de Groot |
spellingShingle |
Vytautas Gapsys Bert L de Groot On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size eLife molecular dynamics simulation statistics thermodynamics kinetics |
author_facet |
Vytautas Gapsys Bert L de Groot |
author_sort |
Vytautas Gapsys |
title |
On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size |
title_short |
On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size |
title_full |
On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size |
title_fullStr |
On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size |
title_full_unstemmed |
On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size |
title_sort |
on the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size |
publisher |
eLife Sciences Publications Ltd |
series |
eLife |
issn |
2050-084X |
publishDate |
2020-08-01 |
description |
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. |
topic |
molecular dynamics simulation statistics thermodynamics kinetics |
url |
https://elifesciences.org/articles/57589 |
work_keys_str_mv |
AT vytautasgapsys ontheimportanceofstatisticsinmolecularsimulationsforthermodynamicskineticsandsimulationboxsize AT bertldegroot ontheimportanceofstatisticsinmolecularsimulationsforthermodynamicskineticsandsimulationboxsize |
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1721458107873230848 |