Molecular dynamics simulations of ionic liquids and electrolytes using polarizable force fields

D Bedrov, JP Piquemal, O Borodin… - Chemical …, 2019 - ACS Publications
Many applications in chemistry, biology, and energy storage/conversion research rely on
molecular simulations to provide fundamental insight into structural and transport properties …

Operando characterization of organic mixed ionic/electronic conducting materials

R Wu, M Matta, BD Paulsen, J Rivnay - Chemical Reviews, 2022 - ACS Publications
Operando characterization plays an important role in revealing the structure–property
relationships of organic mixed ionic/electronic conductors (OMIECs), enabling the direct …

[HTML][HTML] Scalable molecular dynamics on CPU and GPU architectures with NAMD

JC Phillips, DJ Hardy, JDC Maia, JE Stone… - The Journal of …, 2020 - pubs.aip.org
NAMD is a molecular dynamics program designed for high-performance simulations of very
large biological objects on CPU-and GPU-based architectures. NAMD offers scalable …

An empirical polarizable force field based on the classical drude oscillator model: development history and recent applications

JA Lemkul, J Huang, B Roux, AD MacKerell Jr - Chemical reviews, 2016 - ACS Publications
Molecular mechanics force fields that explicitly account for induced polarization represent
the next generation of physical models for molecular dynamics simulations. Several …

[HTML][HTML] sGDML: Constructing accurate and data efficient molecular force fields using machine learning

S Chmiela, HE Sauceda, I Poltavsky, KR Müller… - Computer Physics …, 2019 - Elsevier
We present an optimized implementation of the recently proposed symmetric gradient
domain machine learning (sGDML) model. The sGDML model is able to faithfully reproduce …

Rapid parameterization of small molecules using the force field toolkit

CG Mayne, J Saam, K Schulten… - Journal of …, 2013 - Wiley Online Library
The inability to rapidly generate accurate and robust parameters for novel chemical matter
continues to severely limit the application of molecular dynamics simulations to many …

Biomolecular simulation: a computational microscope for molecular biology

RO Dror, RM Dirks, JP Grossman, H Xu… - Annual review of …, 2012 - annualreviews.org
Molecular dynamics simulations capture the behavior of biological macromolecules in full
atomic detail, but their computational demands, combined with the challenge of …

Transferable, polarizable force field for ionic liquids

K Goloviznina, JN Canongia Lopes… - Journal of chemical …, 2019 - ACS Publications
A general, transferable, polarizable force field for molecular simulation of ionic liquids (ILs)
and their mixtures with molecular compounds is developed. This polarizable model is …

Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields

L Lagardère, LH Jolly, F Lipparini, F Aviat, B Stamm… - Chemical …, 2018 - pubs.rsc.org
We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular
dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) …

Polarizable force field for peptides and proteins based on the classical drude oscillator

PEM Lopes, J Huang, J Shim, Y Luo, H Li… - Journal of chemical …, 2013 - ACS Publications
Presented is a polarizable force field based on a classical Drude oscillator framework,
currently implemented in the programs CHARMM and NAMD, for modeling and molecular …