Water models for biomolecular simulations

AV Onufriev, S Izadi - Wiley Interdisciplinary Reviews …, 2018 - Wiley Online Library
Modern simulation and modeling approaches to investigation of biomolecular structure and
function rely heavily on a variety of methods—water models—to approximate the influence …

Systematic comparison of the structural and dynamic properties of commonly used water models for molecular dynamics simulations

SP Kadaoluwa Pathirannahalage… - Journal of chemical …, 2021 - ACS Publications
Water is a unique solvent that is ubiquitous in biology and present in a variety of solutions,
mixtures, and materials settings. It therefore forms the basis for all molecular dynamics …

Neighbor list artifacts in molecular dynamics simulations

H Kim, B Fábián, G Hummer - Journal of Chemical Theory and …, 2023 - ACS Publications
Molecular dynamics (MD) simulations are widely used in biophysical research. To aid
nonexpert users, most simulation packages provide default values for key input parameters …

[HTML][HTML] Perspective: Atomistic simulations of water and aqueous systems with machine learning potentials

A Omranpour, P Montero De Hijes, J Behler… - The Journal of …, 2024 - pubs.aip.org
As the most important solvent, water has been at the center of interest since the advent of
computer simulations. While early molecular dynamics and Monte Carlo simulations had to …

Molecular perspectives of interfacial properties of the hydrogen+ water mixture in contact with silica or kerogen

Y Yang, AKN Nair, W Zhu, S Sang, S Sun - Journal of Molecular Liquids, 2023 - Elsevier
Interfacial behaviours in multiphase systems containing H 2 are crucial to underground H 2
storage but are not well understood. Molecular dynamics simulations were carried out to …

[HTML][HTML] Vapor–liquid equilibrium of water with the MB-pol many-body potential

MC Muniz, TE Gartner, M Riera, C Knight… - The Journal of …, 2021 - pubs.aip.org
Among the many existing molecular models of water, the MB-pol many-body potential has
emerged as a remarkably accurate model, capable of reproducing thermodynamic …

Accurate simulations of lipid monolayers require a water model with correct surface tension

C Tempra, OHS Ollila… - Journal of Chemical Theory …, 2022 - ACS Publications
Lipid monolayers provide our lungs and eyes their functionality and serve as proxy systems
in biomembrane research. Therefore, lipid monolayers have been studied intensively …

Semi-automated optimization of the CHARMM36 lipid force field to include explicit treatment of long-range dispersion

Y Yu, A Kramer, RM Venable… - Journal of chemical …, 2021 - ACS Publications
The development of the CHARMM lipid force field (FF) can be traced back to the early 1990s
with its current version denoted CHARMM36 (C36). The parametrization of C36 utilized high …

The water-alkane interface at various Nacl salt concentrations: a molecular dynamics study of the readily available force fields

TR Underwood, HC Greenwell - Scientific reports, 2018 - nature.com
In this study, classical molecular dynamic simulations have been used to examine the
molecular properties of the water-alkane interface at various NaCl salt concentrations (up to …

Counterintuitive Trend of Intrusion Pressure with Temperature in the Hydrophobic Cu2(tebpz) MOF

S Merchiori, AL Donne, R Bhatia, M Alvelli, JJ Yu… - Small, 2024 - Wiley Online Library
Liquid porosimetry experiments reveal a peculiar trend of the intrusion pressure of water in
hydrophobic Cu2 (3, 3′, 5, 5′‐tetraethyl‐4, 4′‐bipyrazolate) MOF. At lower temperature …