Reaction Path-Force Matching in Collective Variables: Determining Ab Initio QM/MM Free Energy Profiles by Fitting Mean Force

Biomolecular QM/MM Simulations: What Are Some of the “Burning Issues”?

(2021) Qiang Cui et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Machine Learning in QM/MM Molecular Dynamics Simulations of Condensed-Phase Systems

(2021) Lennard Böselt et al.   Journal of Chemical Theory and Computation

DP-GEN: A concurrent learning platform for the generation of reliable deep learning based potential energy models

(2020) Yuzhi Zhang et al.   COMPUTER PHYSICS COMMUNICATIONS

Development of a Robust Indirect Approach for MM → QM Free Energy Calculations That Combines Force-Matched Reference Potential and Bennett’s Acceptance Ratio Methods

(2019) Timothy J. Giese et al.   Journal of Chemical Theory and Computation

DeePMD-kit: A deep learning package for many-body potential energy representation and molecular dynamics

(2018) Han Wang et al.   COMPUTER PHYSICS COMMUNICATIONS

Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks

(2018) Lin Shen et al.   Journal of Chemical Theory and Computation

Generating Converged Accurate Free Energy Surfaces for Chemical Reactions with a Force-Matched Semiempirical Model

(2018) Matthew P. Kroonblawd et al.   Journal of Chemical Theory and Computation

Accelerating QM/MM Free Energy Computations via Intramolecular Force Matching

(2018) Phillip S. Hudson et al.   Journal of Chemical Theory and Computation

Accelerated Computation of Free Energy Profile at ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semi-Empirical Reference Potential. I. Weighted Thermodynamics Perturbation

(2018) Pengfei Li et al.   Journal of Chemical Theory and Computation

Mapping Free Energy Pathways for ATP Hydrolysis in the E. coli ABC Transporter HlyB by the String Method

(2018) Yan Zhou et al.   MOLECULES

Internal force corrections with machine learning for quantum mechanics/molecular mechanics simulations

(2017) Jingheng Wu et al.   JOURNAL OF CHEMICAL PHYSICS

Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks

(2016) Lin Shen et al.   Journal of Chemical Theory and Computation

QM/MM free energy simulations: recent progress and challenges

(2016) Xiya Lu et al.   MOLECULAR SIMULATION

Using Force-Matched Potentials To Improve the Accuracy of Density Functional Tight Binding for Reactive Conditions

(2015) Nir Goldman et al.   Journal of Chemical Theory and Computation

Reaction Path Force Matching: A New Strategy of Fitting Specific Reaction Parameters for Semiempirical Methods in Combined QM/MM Simulations

(2014) Yan Zhou et al.   Journal of Chemical Theory and Computation

Acceleration of Ab Initio QM/MM Calculations under Periodic Boundary Conditions by Multiscale and Multiple Time Step Approaches

(2014) Kwangho Nam   Journal of Chemical Theory and Computation

Toward an Automatic Determination of Enzymatic Reaction Mechanisms and Their Activation Free Energies

(2013) Kirill Zinovjev et al.   Journal of Chemical Theory and Computation

Semiempirical quantum-chemical methods

(2013) Walter Thiel   Wiley Interdisciplinary Reviews-Computational Molecular Science

Variational calculation of quantum mechanical/molecular mechanical free energy with electronic polarization of solvent

(2012) Hiroshi Nakano et al.   JOURNAL OF CHEMICAL PHYSICS

Multiscale reactive molecular dynamics

(2012) Chris Knight et al.   JOURNAL OF CHEMICAL PHYSICS

Accurate and Efficient Treatment of Continuous Solute Charge Density in the Mean-Field QM/MM Free Energy Calculation

(2012) Hiroshi Nakano et al.   Journal of Chemical Theory and Computation

Optimal scaling factors for CM1 and CM3 atomic charges in RM1-based aqueous simulations

(2011) Jonah Z. Vilseck et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Theoretical models incorporating electron correlation

(2010) John A. Pople et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

Defining Condensed Phase Reactive Force Fields from ab Initio Molecular Dynamics Simulations: The Case of the Hydrated Excess Proton

(2010) Chris Knight et al.   Journal of Chemical Theory and Computation

Exploring Solvent Effects upon the Menshutkin Reaction Using a Polarizable Force Field

(2010) Orlando Acevedo et al.   JOURNAL OF PHYSICAL CHEMISTRY B

QM/MM Methods for Biomolecular Systems

(2009) Hans Martin Senn et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Free Energies of Chemical Reactions in Solution and in Enzymes with Ab Initio Quantum Mechanics/Molecular Mechanics Methods

(2008) Hao Hu et al.   Annual Review of Physical Chemistry

Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: Sequential sampling and optimization on the potential of mean force surface

(2008) Hao Hu et al.   JOURNAL OF CHEMICAL PHYSICS

Developing ab initio quality force fields from condensed phase quantum-mechanics/molecular-mechanics calculations through the adaptive force matching method

(2008) Omololu Akin-Ojo et al.   JOURNAL OF CHEMICAL PHYSICS

The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

(2008) W. G. Noid et al.   JOURNAL OF CHEMICAL PHYSICS

Variational and perturbative formulations of quantum mechanical/molecular mechanical free energy with mean-field embedding and its analytical gradients

(2008) Takeshi Yamamoto   JOURNAL OF CHEMICAL PHYSICS

Fragment Molecular Orbital method-based Molecular Dynamics (FMO-MD) as a simulator for chemical reactions in explicit solvation

(2008) Yuto Komeiji et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY