ArticleeLife2020
On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size.
Article in eLife, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
33 citing papers in PubMed, 76 citations in OpenAlex.
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- System size effects on the free energy landscapes from molecular dynamics of phase-separating bilayers.The Journal of chemical physics · 2024Article
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- Predicting permeation of compounds across the outer membrane of P. aeruginosa using molecular descriptors.Communications chemistry · 2024Article
- Integrating multiscale and machine learning approaches towards the SAMPL9 logPhysical chemistry chemical physics : PCCP · 2024Article
- Guidelines for Free-Energy Calculations Involving Charge Changes.Journal of chemical theory and computation · 2024Article
- Experimental and Theoretical Brownian Dynamics Analysis of Ion Transport During Cellular Electroporation of E. coli Bacteria.Annals of biomedical engineering · 2024Article
- Ensemble-Based Approaches Ensure Reliability and Reproducibility.Journal of chemical information and modeling · 2023Article
- Accurately Predicting Protein pJournal of chemical theory and computation · 2023Article
- Structural Investigation of DHICA Eumelanin Using Density Functional Theory and Classical Molecular Dynamics Simulations.Molecules (Basel, Switzerland) · 2022Article
- Atomic-Level View of the Functional Transition in Vertebrate Hemoglobins: The Case of Antarctic Fish Hbs.Journal of chemical information and modeling · 2022Article
- Implementation of Telescoping Boxes in Adaptive Steered Molecular Dynamics.Journal of chemical theory and computation · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 2 countries.
Funding
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.