Bayesian three-point water models

Abstract We introduce a Bayesian framework leveraging synthetic likelihoods to enable uncertainty quantification and robust inference of non-bonded force parameters in three-point water models. The approach integrates multiple experimental observables—enthalpy of vaporization, molecular volume, the radial distribution function, and hydrogen bonding patterns—to explicitly infer model parameters. Beyond parameter estimation, we quantify uncertainty in both inference observables and validation properties, including those that are difficult to target by other means. By systematically analyzing the response of these observables to parameter variations, our method highlights inherent limitations of three-point water models. These findings highlight the utility of our framework in integrating diverse data sources in a principled uncertainty quantification workflow, ultimately improving confidence in the ability of molecular dynamics simulations to reproduce experimental data. Additionally, we evaluate the performance of the mean and the mode of the posterior distribution, demonstrating the limitations of this family of models.

Authors

Institutions

Publication Details

Journal
npj Computational Materials
Published
2025-11-30
DOI
https://doi.org/10.1038/s41524-025-01879-w
Citations
1
Primary Topic
Protein Structure and Dynamics
Type
article
Field-Weighted Citation Impact
0.81

Funders

Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
OCT
article

Bayesian three-point water models

Stefan Engblom, David van der Spoel, Alfred Nordman
1 citations
npj Computational Materials
Protein Structure and Dynamics
0.81
article

Bayesian three-point water models

Stefan Engblom, David van der Spoel, Alfred Nordman
article en
1 citations

Abstract

Abstract We introduce a Bayesian framework leveraging synthetic likelihoods to enable uncertainty quantification and robust inference of non-bonded force parameters in three-point water models. The approach integrates multiple experimental observables—enthalpy of vaporization, molecular volume, the radial distribution function, and hydrogen bonding patterns—to explicitly infer model parameters. Beyond parameter estimation, we quantify uncertainty in both inference observables and validation properties, including those that are difficult to target by other means. By systematically analyzing the response of these observables to parameter variations, our method highlights inherent limitations of three-point water models. These findings highlight the utility of our framework in integrating diverse data sources in a principled uncertainty quantification workflow, ultimately improving confidence in the ability of molecular dynamics simulations to reproduce experimental data. Additionally, we evaluate the performance of the mean and the mode of the posterior distribution, demonstrating the limitations of this family of models.

npj Computational MaterialsVol. 11(1)
Uppsala University (SE), Science for Life Laboratory (SE)
Kungliga Tekniska Högskolan, Vetenskapsrådet, Uppsala Universitet
Openalex Percentile: Top 21%
Protein Structure and Dynamics
0.81
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.