A simplified charge projection scheme for long-range electrostatics in ab initio QM/MM calculations

Efficient Analytic Second Derivative of Electrostatic Embedding QM/MM Energy: Normal Mode Analysis of Plant Cryptochrome

(2020) Karno Schwinn et al.   Journal of Chemical Theory and Computation

Modern quantum chemistry with [Open]Molcas

(2020) Francesco Aquilante et al.   JOURNAL OF CHEMICAL PHYSICS

Ab initio quantum mechanics/molecular mechanics method with periodic boundaries employing Ewald summation technique to electron-charge interaction: Treatment of the surface-dipole term

(2019) Y. Kawashima et al.   JOURNAL OF CHEMICAL PHYSICS

Analytic gradient for the QM/MM-Ewald method using charges derived from the electrostatic potential: Theory, implementation, and application to ab initio molecular dynamics simulation of the aqueous electron

(2019) Zachary C. Holden et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review

(2019) Aurélien de la Lande et al.   MOLECULES

Analytic QM/MM atomic charge derivatives avoiding the scaling of coupled perturbed equations with the MM subsystem size

(2019) Karno Schwinn et al.   JOURNAL OF CHEMICAL PHYSICS

Are Explicit Solvent Models More Accurate than Implicit Solvent Models? A Case Study on the Menschutkin Reaction

(2019) Junbo Chen et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Multiscale modeling of enzymes: QM-cluster, QM/MM, and QM/MM/MD: A tutorial review

(2018) Shideh Ahmadi et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

Density-Dependent Formulation of Dispersion–Repulsion Interactions in Hybrid Multiscale Quantum/Molecular Mechanics (QM/MM) Models

(2018) Carles Curutchet et al.   Journal of Chemical Theory and Computation

QM/MM Simulations with the Gaussian Electrostatic Model: A Density-based Polarizable Potential

(2018) Hatice Gökcan et al.   Journal of Physical Chemistry Letters

NAMD goes quantum: an integrative suite for hybrid simulations

(2018) Marcelo C R Melo et al.   NATURE METHODS

Exchange-repulsion energy in QM/EFP

(2018) Claudia I. Viquez Rojas et al.   JOURNAL OF CHEMICAL PHYSICS

Tinker 8: Software Tools for Molecular Design

(2018) Joshua A. Rackers et al.   Journal of Chemical Theory and Computation

An Average Solvent Electrostatic Configuration Protocol for QM/MM Free Energy Optimization: Implementation and Application to Rhodopsin Systems

(2017) Yoelvis Orozco-Gonzalez et al.   Journal of Chemical Theory and Computation

Acceleration of Semiempirical QM/MM Methods through Message Passage Interface (MPI), Hybrid MPI/Open Multiprocessing, and Self-Consistent Field Accelerator Implementations

(2017) Pedro Ojeda-May et al.   Journal of Chemical Theory and Computation

A General Route to Include Pauli Repulsion and Quantum Dispersion Effects in QM/MM Approaches

(2017) Tommaso Giovannini et al.   Journal of Chemical Theory and Computation

Averaged Condensed Phase Model for Simulating Molecules in Complex Environments

(2017) Dominique Nocito 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

Ambient-Potential Composite Ewald Method for ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation

(2016) Timothy J. Giese et al.   Journal of Chemical Theory and Computation

Periodic Boundary Conditions in QM/MM Calculations: Implementation and Tests

(2016) Tatiana Vasilevskaya et al.   Journal of Chemical Theory and Computation

LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields

(2016) Eric G. Kratz et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Long-range electrostatic corrections in multipolar/polarizable QM/MM simulations

(2016) Eric G. Kratz et al.   THEORETICAL CHEMISTRY ACCOUNTS

A new smoothing function to introduce long-range electrostatic effects in QM/MM calculations

(2015) Dong Fang et al.   JOURNAL OF CHEMICAL PHYSICS

Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations

(2015) Erich R. Kuechler et al.   JOURNAL OF CHEMICAL PHYSICS

Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method

(2015) Gerhard König et al.   Journal of Chemical Theory and Computation

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

New QM/MM implementation of the DFTB3 method in the gromacs package

(2015) Tomáš Kubař et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Molcas8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table

(2015) Francesco Aquilante et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Development of Multiscale Models for Complex Chemical Systems: From H+H2to Biomolecules (Nobel Lecture)

(2014) Martin Karplus   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Multiscale Modeling of Biological Functions: From Enzymes to Molecular Machines (Nobel Lecture)

(2014) Arieh Warshel   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

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

The CHARMM-TURBOMOLE interface for efficient and accurate QM/MM molecular dynamics, free energies, and excited state properties

(2014) Saleh Riahi et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

(2014) Yihan Shao et al.   MOLECULAR PHYSICS

Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Methods in Computational Enzymology

(2013) Marc W. van der Kamp et al.   BIOCHEMISTRY

Classical Electrostatics for Biomolecular Simulations

(2013) G. Andrés Cisneros et al.   CHEMICAL REVIEWS

Periodic boundary conditions for QM/MM calculations: Ewald summation for extended Gaussian basis sets

(2013) Zachary C. Holden et al.   JOURNAL OF CHEMICAL PHYSICS

QuanPol: A full spectrum and seamless QM/MM program

(2013) Nandun M. Thellamurege et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

An extensible interface for QM/MM molecular dynamics simulations with AMBER

(2013) Andreas W. Götz et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

The dispersion interaction between quantum mechanics and effective fragment potential molecules

(2012) Quentin A. Smith et al.   JOURNAL OF CHEMICAL PHYSICS

A Modified QM/MM Hamiltonian with the Self-Consistent-Charge Density-Functional-Tight-Binding Theory for Highly Charged QM Regions

(2012) Guanhua Hou 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

Tuned and Balanced Redistributed Charge Scheme for Combined Quantum Mechanical and Molecular Mechanical (QM/MM) Methods and Fragment Methods: Tuning Based on the CM5 Charge Model

(2012) Bo Wang et al.   Journal of Chemical Theory and Computation

Electronic Properties of Water in Liquid Environment. A Sequential QM/MM Study Using the Free Energy Gradient Method

(2012) Herbert C. Georg et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Unique QM/MM potential energy surface exploration using microiterations

(2011) Federico Melaccio et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

Efficient solvent boundary potential for hybrid potential simulations

(2011) Alexey Aleksandrov et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Long-Range Electrostatic Effects in QM/MM Studies of Enzymatic Reactions: Application of the Solvated Macromolecule Boundary Potential

(2010) Tobias Benighaus et al.   Journal of Chemical Theory and Computation

A minimal implementation of the AMBER-GAUSSIAN interface for ab initio QM/MM-MD simulation

(2010) Takuya Okamoto et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

An efficient implementation of a QM–MM method in SIESTA

(2010) Carlos F. Sanz-Navarro et al.   THEORETICAL CHEMISTRY ACCOUNTS

QM/MM Methods for Biomolecular Systems

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

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

A General Boundary Potential for Hybrid QM/MM Simulations of Solvated Biomolecular Systems

(2009) Tobias Benighaus et al.   Journal of Chemical Theory and Computation

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

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

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS

Efficiency and Accuracy of the Generalized Solvent Boundary Potential for Hybrid QM/MM Simulations: Implementation for Semiempirical Hamiltonians

(2008) Tobias Benighaus et al.   Journal of Chemical Theory and Computation

Accelerating QM/MM Free Energy Calculations:  Representing the Surroundings by an Updated Mean Charge Distribution

(2008) Edina Rosta et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The implementation of a fast and accurate QM/MM potential method in Amber

(2007) Ross C. Walker et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY