NAMD goes quantum: an integrative suite for hybrid simulations

Chromophore twisting in the excited state of a photoswitchable fluorescent protein captured by time-resolved serial femtosecond crystallography

(2017) Nicolas Coquelle et al.   Nature Chemistry

Software update: the ORCA program system, version 4.0

(2017) Frank Neese   Wiley Interdisciplinary Reviews-Computational Molecular Science

Sparse maps—A systematic infrastructure for reduced-scaling electronic structure methods. II. Linear scaling domain based pair natural orbital coupled cluster theory

(2016) Christoph Riplinger et al.   JOURNAL OF CHEMICAL PHYSICS

Extended Adaptive Biasing Force Algorithm. An On-the-Fly Implementation for Accurate Free-Energy Calculations

(2016) Haohao Fu et al.   Journal of Chemical Theory and Computation

How Large Should the QM Region Be in QM/MM Calculations? The Case of Catechol O-Methyltransferase

(2016) Heather J. Kulik et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Exploring the Dependence of QM/MM Calculations of Enzyme Catalysis on the Size of the QM Region

(2016) Garima Jindal et al.   JOURNAL OF PHYSICAL CHEMISTRY B

QwikMD — Integrative Molecular Dynamics Toolkit for Novices and Experts

(2016) João V. Ribeiro et al.   Scientific Reports

Mapping Mechanical Force Propagation through Biomolecular Complexes

(2015) Constantin Schoeler et al.   NANO LETTERS

RM1 Semiempirical Quantum Chemistry: Parameters for Trivalent Lanthanum, Cerium and Praseodymium

(2015) José Diogo L. Dutra et al.   PLoS One

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

Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD

(2013) Wei Jiang et al.   COMPUTER PHYSICS COMMUNICATIONS

Convergence of QM/MM and Cluster Models for the Spectroscopic Properties of the Oxygen-Evolving Complex in Photosystem II

(2013) Marius Retegan et al.   Journal of Chemical Theory and Computation

Corrected small basis set Hartree-Fock method for large systems

(2013) Rebecca Sure 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

Hybrid QM/MM Molecular Dynamics Study of Benzocaine in a Membrane Environment: How Does a Quantum Mechanical Treatment of Both Anesthetic and Lipids Affect Their Interaction

(2012) Rafael C. Bernardi et al.   Journal of Chemical Theory and Computation

Generating Efficient Quantum Chemistry Codes for Novel Architectures

(2012) Alexey V. Titov et al.   Journal of Chemical Theory and Computation

GPU Linear Algebra Libraries and GPGPU Programming for Accelerating MOPAC Semiempirical Quantum Chemistry Calculations

(2012) Julio Daniel Carvalho Maia 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

Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters

(2012) James J. P. Stewart   JOURNAL OF MOLECULAR MODELING

Exit Strategies for Charged tRNA from GluRS

(2010) Alexis Black Pyrkosz et al.   JOURNAL OF MOLECULAR BIOLOGY

QM/MM Methods for Biomolecular Systems

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

Dynamical networks in tRNA:protein complexes

(2009) A. Sethi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Finding Transition Pathways Using the String Method with Swarms of Trajectories

(2008) Albert C. Pan 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