Multi-level free energy simulation with a staged transformation approach

Machine learning approaches for analyzing and enhancing molecular dynamics simulations

(2020) Yihang Wang et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The Good, the Bad, and the Ugly: “HiPen”, a New Dataset for Validating (S)QM/MM Free Energy Simulations

(2019) Fiona Kearns et al.   MOLECULES

Host–Guest Relative Binding Affinities at Density-Functional Theory Level from Semiempirical Molecular Dynamics Simulations

(2019) Meiting Wang et al.   Journal of Chemical Theory and Computation

On the use of interaction energies in QM/MM free energy simulations

(2019) Phillip S. Hudson et al.   Journal of Chemical Theory and Computation

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

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

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

On the convergence of multi-scale free energy simulations

(2018) Gerhard König et al.   MOLECULAR SIMULATION

Efficient Computation of Free Energy Surfaces of Diels–Alder Reactions in Explicit Solvent at Ab Initio QM/MM Level

(2018) Pengfei Li et al.   MOLECULES

Perspective: Identification of collective variables and metastable states of protein dynamics

(2018) Florian Sittel et al.   JOURNAL OF CHEMICAL PHYSICS

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

How Many Conformations Need To Be Sampled To Obtain Converged QM/MM Energies? The Curse of Exponential Averaging

(2017) Ulf Ryde   Journal of Chemical Theory and Computation

Computing converged free energy differences between levels of theory via nonequilibrium work methods: Challenges and opportunities

(2017) Fiona L. Kearns et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications

(2016) Anders S. Christensen et al.   CHEMICAL REVIEWS

Perspective: Quantum mechanical methods in biochemistry and biophysics

(2016) Qiang Cui   JOURNAL OF CHEMICAL PHYSICS

Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level

(2016) Martin A. Olsson et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Convergence of single-step free energy perturbation

(2016) Stefan Boresch et al.   MOLECULAR PHYSICS

QM/MM free energy simulations: recent progress and challenges

(2016) Xiya Lu et al.   MOLECULAR SIMULATION

Correcting for the free energy costs of bond or angle constraints in molecular dynamics simulations

(2015) Gerhard König et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States

(2015) Elizabeth Brunk et al.   CHEMICAL REVIEWS

Improving intermolecular interactions in DFTB3 using extended polarization from chemical-potential equalization

(2015) Anders S. Christensen et al.   JOURNAL OF CHEMICAL PHYSICS

QM/MM Modelling of Drug-Metabolizing Enzymes

(2014) Richard Lonsdale et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes

(2014) Gerhard König et al.   Journal of Chemical Theory and Computation

Quantum mechanics/molecular mechanics dual Hamiltonian free energy perturbation

(2013) Iakov Polyak et al.   JOURNAL OF CHEMICAL PHYSICS

A Variational Linear-Scaling Framework to Build Practical, Efficient Next-Generation Orbital-Based Quantum Force Fields

(2013) Timothy J. Giese et al.   Journal of Chemical Theory and Computation

Density functional tight binding: application to organic and biological molecules

(2013) Michael Gaus et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Parametrization and Benchmark of DFTB3 for Organic Molecules

(2012) Michael Gaus et al.   Journal of Chemical Theory and Computation

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

Extended Polarization in Third-Order SCC-DFTB from Chemical-Potential Equalization

(2012) Steve Kaminski et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations

(2012) Jimmy Heimdal et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Solvation Dynamics and Proton Transfer in Nanoconfined Liquids

(2011) Ward H. Thompson   Annual Review of Physical Chemistry

DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB)

(2011) Michael Gaus et al.   Journal of Chemical Theory and Computation

Paradynamics: An Effective and Reliable Model for Ab Initio QM/MM Free-Energy Calculations and Related Tasks

(2011) Nikolay V. Plotnikov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Metadynamics

(2011) Alessandro Barducci et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Free energy calculations using dual-level Born–Oppenheimer molecular dynamics

(2010) Marius Retegan et al.   JOURNAL OF CHEMICAL PHYSICS

Efficiency of alchemical free energy simulations. I. A practical comparison of the exponential formula, thermodynamic integration, and Bennett's acceptance ratio method

(2010) Stefan Bruckner et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Good Practices in Free-Energy Calculations

(2010) Andrew Pohorille et al.   JOURNAL OF PHYSICAL CHEMISTRY B

P450 Enzymes: Their Structure, Reactivity, and Selectivity—Modeled by QM/MM Calculations

(2009) Sason Shaik et al.   CHEMICAL REVIEWS

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

(2009) K. Vanommeslaeghe et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM: The biomolecular simulation program

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

Computations of Standard Binding Free Energies with Molecular Dynamics Simulations

(2009) Yuqing Deng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Hybrid atomistic simulation methods for materials systems

(2009) N Bernstein et al.   REPORTS ON PROGRESS IN PHYSICS

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

Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit

(2008) H. Lee Woodcock et al.   JOURNAL OF CHEMICAL PHYSICS