Adaptive free energy sampling in multidimensional collective variable space using boxed molecular dynamics

Communication: Real time observation of unimolecular decay of Criegee intermediates to OH radical products

(2016) Yi Fang et al.   JOURNAL OF CHEMICAL PHYSICS

Role of Molecular Dynamics and Related Methods in Drug Discovery

(2016) Marco De Vivo et al.   JOURNAL OF MEDICINAL CHEMISTRY

Fully Atomistic Simulations of Protein Unfolding in Low Speed Atomic Force Microscope and Force Clamp Experiments with the Help of Boxed Molecular Dynamics

(2016) Jonathan J. Booth et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The Study of Reactive Intermediates in Condensed Phases

(2016) Barry K. Carpenter et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Theoretical Chemical Kinetics in Tropospheric Chemistry: Methodologies and Applications

(2015) Luc Vereecken et al.   CHEMICAL REVIEWS

Non-equilibrium reaction and relaxation dynamics in a strongly interacting explicit solvent: F + CD3CN treated with a parallel multi-state EVB model

(2015) David R. Glowacki et al.   JOURNAL OF CHEMICAL PHYSICS

Markov state modeling and dynamical coarse-graining via discrete relaxation path sampling

(2015) B. Fačkovec et al.   JOURNAL OF CHEMICAL PHYSICS

Simultaneous estimation of free energies and rates using forward flux sampling and mean first passage times

(2015) Vikram Thapar et al.   JOURNAL OF CHEMICAL PHYSICS

Vibrational relaxation and microsolvation of DF after F-atom reactions in polar solvents

(2015) G. T. Dunning et al.   SCIENCE

Perspective: Bimolecular chemical reaction dynamics in liquids

(2014) Andrew J. Orr-Ewing   JOURNAL OF CHEMICAL PHYSICS

The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask

(2014) Jeffrey Comer et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Unraveling the Factors That Control Soft Landing of Small Silyl Ions on Fluorinated Self-Assembled Monolayers

(2014) Juan José Nogueira et al.   Journal of Physical Chemistry C

Recent applications of boxed molecular dynamics: a simple multiscale technique for atomistic simulations

(2014) J. Booth et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Adaptive single replica multiple state transition interface sampling

(2013) Wei-Na Du et al.   JOURNAL OF CHEMICAL PHYSICS

Systematic exploration of the mechanism of chemical reactions: the global reaction route mapping (GRRM) strategy using the ADDF and AFIR methods

(2013) Satoshi Maeda et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Efficient Numerical Reconstruction of Protein Folding Kinetics with Partial Path Sampling and Pathlike Variables

(2013) J. Juraszek et al.   PHYSICAL REVIEW LETTERS

Unraveling the role of protein dynamics in dihydrofolate reductase catalysis

(2013) L. Y. P. Luk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Peptide kinetics from picoseconds to microseconds using boxed molecular dynamics: Power law rate coefficients in cyclisation reactions

(2012) Dmitrii V. Shalashilin et al.   JOURNAL OF CHEMICAL PHYSICS

An adaptive weighted ensemble procedure for efficient computation of free energies and first passage rates

(2012) Divesh Bhatt et al.   JOURNAL OF CHEMICAL PHYSICS

Thermodynamics and kinetics of bubble nucleation: Simulation methodology

(2012) Stacey L. Meadley et al.   JOURNAL OF CHEMICAL PHYSICS

On Reaction Coordinate Optimality

(2012) Sergei V. Krivov   Journal of Chemical Theory and Computation

MESMER: An Open-Source Master Equation Solver for Multi-Energy Well Reactions

(2012) David R. Glowacki et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Molecular Simulations of Wetting of a Rough Surface by an Oily Fluid: Effect of Topology, Chemistry, and Droplet Size on Wetting Transition Rates

(2012) Elizabeth S. Savoy et al.   LANGMUIR

Simulation Study of Free-Energy Barriers in the Wetting Transition of an Oily Fluid on a Rough Surface with Reentrant Geometry

(2012) Elizabeth S. Savoy et al.   LANGMUIR

Taking Ockham's razor to enzyme dynamics and catalysis

(2012) David R. Glowacki et al.   Nature Chemistry

Reaction dynamics of CN radicals with tetrahydrofuran in liquid solutions

(2012) R. A. Rose et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Simulating Chemistry Using Quantum Computers

(2011) Ivan Kassal et al.   Annual Review of Physical Chemistry

Accelerating chemical reactions: Exploring reactive free-energy surfaces using acceleratedab initiomolecular dynamics

(2011) Levi C. T. Pierce et al.   JOURNAL OF CHEMICAL PHYSICS

Product energy deposition of CN + alkane H abstraction reactions in gas and solution phases

(2011) David R. Glowacki et al.   JOURNAL OF CHEMICAL PHYSICS

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

Boxed Molecular Dynamics: Decorrelation Time Scales and the Kinetic Master Equation

(2011) David R. Glowacki et al.   Journal of Chemical Theory and Computation

Chemical Reaction Dynamics in Liquid Solutions

(2011) Andrew J. Orr-Ewing et al.   Journal of Physical Chemistry Letters

Ultrafast energy flow in the wake of solution-phase bimolecular reactions

(2011) David R. Glowacki et al.   Nature Chemistry

Vibrationally Quantum-State-Specific Reaction Dynamics of H Atom Abstraction by CN Radical in Solution

(2011) S. J. Greaves et al.   SCIENCE

Unimolecular Reactions of Peroxy Radicals in Atmospheric Chemistry and Combustion

(2010) David R. Glowacki et al.   CHEMPHYSCHEM

Adaptive Steered Molecular Dynamics of the Long-Distance Unfolding of Neuropeptide Y

(2010) Gungor Ozer et al.   Journal of Chemical Theory and Computation

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

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

Pitfalls of choosing an order parameter for rare event calculations

(2009) Bradley M. Dickson et al.   JOURNAL OF CHEMICAL PHYSICS

Markovian milestoning with Voronoi tessellations

(2009) Eric Vanden-Eijnden et al.   JOURNAL OF CHEMICAL PHYSICS

CHARMM: The biomolecular simulation program

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

Boxed Molecular Dynamics: A Simple and General Technique for Accelerating Rare Event Kinetics and Mapping Free Energy in Large Molecular Systems

(2009) David R. Glowacki et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Graphical Processing Units for Quantum Chemistry

(2008) Ivan S. Ufimtsev et al.   COMPUTING IN SCIENCE & ENGINEERING

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