Center for Molecular Modeling - D. Fauconnier

STable AutoCorrelation Integral Estimator: Robust and Accurate Transport Properties from Molecular Dynamics Simulations

toon — Thu, 22 Jan 2026 11:14:40 +0000

G. Toraman, D. Fauconnier, T. Verstraelen

Journal of Chemical Information and Modeling (JCIM)

65(19), pp. 10445-10464

2025

Abstract

STACIE (STable AutoCorrelation Integral Estimator) is a novel algorithm and Python package that delivers robust, uncertainty-aware estimates of autocorrelation integrals from time-correlated data. While its primary application is deriving transport properties from equilibrium molecular dynamics simulations, STACIE is equally applicable to time-correlated data in other scientific fields. A key feature of STACIE is its ability to provide robust and accurate estimates without requiring manual adjustment of hyperparameters. Additionally, one can follow a simple protocol to prepare sufficient simulation data to achieve a desired relative error of the transport property. We demonstrate its application by estimating the ionic electrical conductivity of a NaCl-water electrolyte solution. We also present a massive synthetic benchmark data set to rigorously validate STACIE, comprising 15,360 sets of time-correlated inputs generated with diverse covariance kernels with known autocorrelation integrals. STACIE is open source and available on GitHub and PyPI, with comprehensive documentation and examples.

Open Access version available at UGent repository

Gold Open Access

DOI

https://doi.org/10.1021/acs.jcim.5c01475

Impact of Ad Hoc Post-Processing Parameters on the Lubricant Viscosity Calculated with Equilibrium Molecular Dynamics Simulations

leen — Thu, 20 Apr 2023 08:37:33 +0000

G. Toraman, T. Verstraelen, D. Fauconnier

Lubricants

11, 4, 183

2023

Abstract

Viscosity is a crucial property of liquid lubricants, and it is theoretically a well-defined quantity in molecular dynamics (MD) simulations. However, no standardized protocol has been defined for calculating this property from equilibrium MD simulations. While best practices do exist, the actual calculation depends on several ad hoc decisions during the post-processing of the raw MD data. A common protocol for calculating the viscosity with equilibrium MD simulations is called the time decomposition method (TDM). Although the TDM attempts to standardize the viscosity calculation using the Green–Kubo method, it still relies on certain empirical rules and subjective user observations, e.g., the plateau region of the Green–Kubo integral or the integration cut-off time. It is known that the TDM works reasonably well for low-viscosity fluids, e.g., at high temperatures. However, modified heuristics have been proposed at high pressures, indicating that no single set of rules works well for all circumstances. This study examines the effect of heuristics and ad hoc decisions on the predicted viscosity of a short, branched lubricant molecule, 2,2,4-trimethylhexane. Equilibrium molecular dynamics simulations were performed at various operating conditions (high pressures and temperatures), followed by post-processing with three levels of uncertainty quantification. A new approach, “Enhanced Bootstrapping”, is introduced to assess the effects of individual ad hoc parameters on the viscosity. The results show a strong linear correlation (with a Pearson correlation coefficient of up to 36%) between the calculated viscosity and an ad hoc TDM parameter, which determines the integration cut-off time, under realistic lubrication conditions, particularly at high pressures. This study reveals that ad hoc decisions can lead to potentially misleading conclusions when the post-processing is performed ambiguously.

Green Open Access

DOI

https://doi.org/10.3390/lubricants11040183

Private attachment

lubricants-11-00183.pdf

Robust Derivation of Uncertainties, Correlation Times, and Transport Properties from Molecular Dynamics Simulations: A Force Field Validation Study on Squalane

toon — Thu, 22 Jan 2026 11:09:18 +0000

R. Bohy, G. Toraman, D. Fauconnier, T. Verstraelen

ISBN/ISSN:

Poster

Brussel, Belgium

Friday, 12 December, 2025

Conference reference

First Symposium on Computational Chemistry in Flanders: Computational Design of Drugs and Materials

Transport Properties, Correlation Times, and Uncertainties in Molecular Dynamics Simulations with the STable AutoCorrelation Integral Estimator Applied to Squalane

toon — Thu, 22 Jan 2026 11:04:37 +0000

R. Bohy, G. Toraman, D. Fauconnier, T. Verstraelen

ISBN/ISSN:

Poster

Amsterdam, The Netherlands

Monday, 5 January, 2026 to Friday, 16 January, 2026

Conference reference

MolSim 2026

Simulation of thermo-mechanical properties of Environmentally Acceptable Lubricants

leen — Thu, 17 Mar 2022 20:43:40 +0000

Quantitative predictions of density and viscosity through force matching

leen — Thu, 17 Mar 2022 20:35:58 +0000

Nanoscale simulations of lubricants and lubricant additives

leen — Mon, 15 Mar 2021 08:14:28 +0000

Simulation of lubricant properties in gear and bearing contacts

leen — Mon, 15 Mar 2021 07:46:49 +0000

Nanoscale simulations of lubricants and lubricant additives?

samuel — Thu, 05 Mar 2020 11:04:37 +0000

Simulation of lubricants behaviour in gear and bearing contacts

samuel — Mon, 02 Mar 2020 13:11:09 +0000