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

Polarizable Molecular Dynamics in a Polarizable Continuum Solvent

(2015) Filippo Lipparini et al.   Journal of Chemical Theory and Computation

Achieving Linear Scaling in Computational Cost for a Fully Polarizable MM/Continuum Embedding

(2015) Stefano Caprasecca et al.   Journal of Chemical Theory and Computation

Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II. Toward Massively Parallel Computations Using Smooth Particle Mesh Ewald

(2015) Louis Lagardère et al.   Journal of Chemical Theory and Computation

Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model

(2015) Marie L. Laury et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Octahedral point-charge model and its application to fragment molecular orbital calculations of chemical shifts

(2014) Qi Gao et al.   CHEMICAL PHYSICS LETTERS

Charge Anisotropy: Where Atomic Multipoles Matter Most

(2014) Christian Kramer et al.   Journal of Chemical Theory and Computation

Toward QM/MM Simulation of Enzymatic Reactions with the Drude Oscillator Polarizable Force Field

(2014) Eliot Boulanger et al.   Journal of Chemical Theory and Computation

A Novel, Computationally Efficient Multipolar Model Employing Distributed Charges for Molecular Dynamics Simulations

(2014) Mike Devereux et al.   Journal of Chemical Theory and Computation

Challenges within the Linear Response Approximation When Studying Enzyme Catalysis and Effects of Mutations

(2014) Avital Sharir-Ivry et al.   Journal of Chemical Theory and Computation

Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: I. Toward Massively Parallel Direct Space Computations

(2014) Filippo Lipparini et al.   Journal of Chemical Theory and Computation

GEM*: A Molecular Electronic Density-Based Force Field for Molecular Dynamics Simulations

(2014) Robert E. Duke et al.   Journal of Chemical Theory and Computation

Geometry Optimization in Polarizable QM/MM Models: The Induced Dipole Formulation

(2014) Stefano Caprasecca et al.   Journal of Chemical Theory and Computation

S/G-1: An ab Initio Force-Field Blending Frozen Hermite Gaussian Densities and Distributed Multipoles. Proof of Concept and First Applications to Metal Cations

(2014) Robin Chaudret et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Multiple Environment Single System Quantum Mechanical/Molecular Mechanical (MESS-QM/MM) Calculations. 1. Estimation of Polarization Energies

(2014) Alexander J. Sodt et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Projected Hybrid Orbitals: A General QM/MM Method

(2014) Yingjie Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Hybrid QM/MM Simulation Study of Intramolecular Proton Transfer in the Pyridoxal 5′-Phosphate in the Active Site of Transaminase: Influence of Active Site Interaction on Proton Transfer

(2014) Sindrila Dutta Banik et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

(2014) Yihan Shao et al.   MOLECULAR PHYSICS

Classical Electrostatics for Biomolecular Simulations

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

A gauge invariant multiscale approach to magnetic spectroscopies in condensed phase: General three-layer model, computational implementation and pilot applications

(2013) Filippo Lipparini et al.   JOURNAL OF CHEMICAL PHYSICS

Mean field QM/MM method: Average position approximation

(2013) Fengchao Cui et al.   JOURNAL OF CHEMICAL PHYSICS

Toward a Deeper Understanding of Enzyme Reactions Using the Coupled ELF/NCI Analysis: Application to DNA Repair Enzymes

(2013) Dong Fang et al.   Journal of Chemical Theory and Computation

Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins

(2013) Yue Shi et al.   Journal of Chemical Theory and Computation

QuanPol: A full spectrum and seamless QM/MM program

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

Tests of an Adaptive QM/MM Calculation on Free Energy Profiles of Chemical Reactions in Solution

(2013) Csilla Várnai et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Systematic Improvement of a Classical Molecular Model of Water

(2013) Lee-Ping Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Ab Initio QM/MM Calculations Show an Intersystem Crossing in the Hydrogen Abstraction Step in Dealkylation Catalyzed by AlkB

(2013) Dong Fang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Ultrafast Quantum Mechanics/Molecular Mechanics Monte Carlo simulations using generalized multipole polarizabilities

(2012) Tomasz Janowski et al.   CHEMICAL PHYSICS LETTERS

Analytical First and Second Derivatives for a Fully Polarizable QM/Classical Hamiltonian

(2012) Filippo Lipparini et al.   Journal of Chemical Theory and Computation

Linear Response Theory and Electronic Transition Energies for a Fully Polarizable QM/Classical Hamiltonian

(2012) Filippo Lipparini et al.   Journal of Chemical Theory and Computation

Application of Gaussian Electrostatic Model (GEM) Distributed Multipoles in the AMOEBA Force Field

(2012) G. Andrés Cisneros   Journal of Chemical Theory and Computation

Toward a Unified Modeling of Environment and Bridge-Mediated Contributions to Electronic Energy Transfer: A Fully Polarizable QM/MM/PCM Approach

(2012) Stefano Caprasecca et al.   Journal of Chemical Theory and Computation

Solvent Boundary Potentials for Hybrid QM/MM Computations Using Classical Drude Oscillators: A Fully Polarizable Model

(2012) Eliot Boulanger et al.   Journal of Chemical Theory and Computation

A valence bond model for aqueous Cu(II) and Zn(II) ions in the AMOEBA polarizable force field

(2012) Jin Yu Xiang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Analytic energy gradients in combined second order Møller-Plesset perturbation theory and conductorlike polarizable continuum model calculation

(2011) Dejun Si et al.   JOURNAL OF CHEMICAL PHYSICS

MSCALE: A General Utility for Multiscale Modeling

(2011) H. Lee Woodcock et al.   Journal of Chemical Theory and Computation

Solvation Effects on Electronic Transitions: Exploring the Performance of Advanced Solvent Potentials in Polarizable Embedding Calculations

(2011) Tobias Schwabe et al.   Journal of Chemical Theory and Computation

The Significance of Parameters in Charge Equilibration Models

(2011) T. Verstraelen et al.   Journal of Chemical Theory and Computation

On the effect of a variation of the force field, spatial boundary condition and size of the QM region in QM/MM MD simulations

(2011) Katharina Meier et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Analytic Energy Gradient in Combined Second-Order Møller–Plesset Perturbation Theory and Polarizable Force Field Calculation

(2011) Hui Li   JOURNAL OF PHYSICAL CHEMISTRY A

Benchmark Structures and Binding Energies of Small Water Clusters with Anharmonicity Corrections

(2011) Berhane Temelso et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Excitation Energies in Solution: The Fully Polarizable QM/MM/PCM Method

(2011) Arnfinn Hykkerud Steindal et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Correlation between electron localization and metal ion mutagenicity in DNA synthesis from QM/MM calculations

(2011) Robin Chaudret et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Psi4: an open-source ab initio electronic structure program

(2011) Justin M. Turney et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations

(2010) M. Valiev et al.   COMPUTER PHYSICS COMMUNICATIONS

A second generation distributed point polarizable water model

(2010) Revati Kumar et al.   JOURNAL OF CHEMICAL PHYSICS

Development of a Polarizable Force Field Using Multiple Fluctuating Charges per Atom

(2010) Dong-Xia Zhao et al.   Journal of Chemical Theory and Computation

Excited States in Solution through Polarizable Embedding

(2010) Jógvan Magnus Olsen et al.   Journal of Chemical Theory and Computation

Polarizable Molecular Dynamics Simulation of Zn(II) in Water Using the AMOEBA Force Field

(2010) Johnny C. Wu et al.   Journal of Chemical Theory and Computation

QM/MM Methods for Biomolecular Systems

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

Electronic Energy Transfer in Condensed Phase Studied by a Polarizable QM/MM Model

(2009) Carles Curutchet et al.   Journal of Chemical Theory and Computation

Catalytic mechanism of human DNA polymerase λ with Mg2+ and Mn2+ from ab initio quantum mechanical/molecular mechanical studies

(2008) G. Andrés Cisneros et al.   DNA REPAIR

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

Hybrid ab initio Kohn-Sham density functional theory/frozen-density orbital-free density functional theory simulation method suitable for biological systems

(2008) Miroslav Hodak et al.   JOURNAL OF CHEMICAL PHYSICS

A pseudobond parametrization for improved electrostatics in quantum mechanical/molecular mechanical simulations of enzymes

(2008) Jerry M. Parks et al.   JOURNAL OF CHEMICAL PHYSICS