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

A molecular dynamics study of intramolecular proton transfer reaction of malonaldehyde in solutions based upon mixed quantum-classical approximation. I. Proton transfer reaction in water

(2014) Atsushi Yamada et al.   JOURNAL OF CHEMICAL PHYSICS

Projected Hybrid Orbitals: A General QM/MM Method

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

Accurate Modeling of Organic Molecular Crystals by Dispersion-Corrected Density Functional Tight Binding (DFTB)

(2014) Jan Gerit Brandenburg et al.   Journal of Physical Chemistry Letters

Steric and electrostatic effects on photoisomerization dynamics using QM/MM ab initio multiple spawning

(2014) Aaron M. Virshup et al.   THEORETICAL CHEMISTRY ACCOUNTS

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

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

Ultrafast photochemistry of Anabaena Sensory Rhodopsin: Experiment and theory

(2013) Igor Schapiro et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Free-energy analyses of a proton transfer reaction by simulated-tempering umbrella sampling and first-principles molecular dynamics simulations

(2013) Yoshiharu Mori et al.   PHYSICAL REVIEW E

Density functional tight binding: application to organic and biological molecules

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

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

Density-functional tight binding-an approximate density-functional theory method

(2012) Gotthard Seifert et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Conformational Discrepancies Between Molecular Dynamics Force Fields and Vibrational Spectroscopy in Short Alanine-Based Peptides

(2011) Daniel Verbaro et al.   BIOPHYSICAL JOURNAL

Lagrangian formulation with dissipation of Born-Oppenheimer molecular dynamics using the density-functional tight-binding method

(2011) Guishan Zheng et al.   JOURNAL OF CHEMICAL PHYSICS

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

Kinetics of cyclobutane thymine dimer splitting by DNA photolyase directly monitored in the UV

(2011) V. Thiagarajan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamics and mechanism of cyclobutane pyrimidine dimer repair by DNA photolyase

(2011) Z. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metadynamics

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

A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu

(2010) Stefan Grimme et al.   JOURNAL OF CHEMICAL PHYSICS

Proton Transfer Studied Using a Combined Ab Initio Reactive Potential Energy Surface with Quantum Path Integral Methodology

(2010) Kim F. Wong et al.   Journal of Chemical Theory and Computation

QM/MM Methods for Biomolecular Systems

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

Evaluating the Performance of the ff99SB Force Field Based on NMR Scalar Coupling Data

(2009) Lauren Wickstrom et al.   BIOPHYSICAL JOURNAL

Density-functional tight-binding for beginners

(2009) Pekka Koskinen et al.   COMPUTATIONAL MATERIALS SCIENCE

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

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

Are Current Semiempirical Methods Better Than Force Fields? A Study from the Thermodynamics Perspective†

(2009) Gustavo de M. Seabra et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Color-Tuning Mechanism of Firefly Investigated by Multi-Configurational Perturbation Method

(2009) Isabelle Navizet et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Computational Study of Thymine Dimer Radical Anion Splitting in the Self-Repair Process of Duplex DNA

(2008) Fanny Masson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

(2008) Alessandro Laio et al.   REPORTS ON PROGRESS IN PHYSICS

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

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