Internal force corrections with machine learning for quantum mechanics/molecular mechanics simulations

Efficient free energy calculations by combining two complementary tempering sampling methods

(2017) Liangxu Xie et al.   JOURNAL OF CHEMICAL PHYSICS

Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks

(2016) Lin Shen et al.   Journal of Chemical Theory and Computation

Machine Learning Force Fields: Construction, Validation, and Outlook

(2016) V. Botu et al.   Journal of Physical Chemistry C

QM/MM free energy simulations: recent progress and challenges

(2016) Xiya Lu et al.   MOLECULAR SIMULATION

Machine learning exciton dynamics

(2016) Florian Häse et al.   Chemical Science

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

Dynamics and Kinetics Study of “In-Water” Chemical Reactions by Enhanced Sampling of Reactive Trajectories

(2015) Jun Zhang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Conformational Preadjustment in Aqueous Claisen Rearrangement Revealed by SITS-QM/MM MD Simulations

(2015) Jun Zhang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Learning scheme to predict atomic forces and accelerate materials simulations

(2015) V. Botu et al.   PHYSICAL REVIEW B

Molecular Dynamics with On-the-Fly Machine Learning of Quantum-Mechanical Forces

(2015) Zhenwei Li et al.   PHYSICAL REVIEW LETTERS

Collective Variable Approaches for Single Molecule Flexible Fitting and Enhanced Sampling

(2014) Harish Vashisth et al.   CHEMICAL REVIEWS

Combine umbrella sampling with integrated tempering method for efficient and accurate calculation of free energy changes of complex energy surface

(2014) Mingjun Yang et al.   JOURNAL OF CHEMICAL PHYSICS

Free Energy Surface Reconstruction from Umbrella Samples Using Gaussian Process Regression

(2014) Thomas Stecher et al.   Journal of Chemical Theory and Computation

Reaction Path Force Matching: A New Strategy of Fitting Specific Reaction Parameters for Semiempirical Methods in Combined QM/MM Simulations

(2014) Yan Zhou et al.   Journal of Chemical Theory and Computation

Using collective variables to drive molecular dynamics simulations

(2013) Giacomo Fiorin et al.   MOLECULAR PHYSICS

Some recent techniques for free energy calculations

(2009) Eric Vanden-Eijnden   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

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

Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes

(2008) Hao Hu et al.   JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM

Highly Dissociative and Concerted Mechanism for the Nicotinamide Cleavage Reaction in Sir2Tm Enzyme Suggested by Ab Initio QM/MM Molecular Dynamics Simulations

(2008) Po Hu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

How Do SET-Domain Protein Lysine Methyltransferases Achieve the Methylation State Specificity? Revisited by Ab Initio QM/MM Molecular Dynamics Simulations

(2008) Po Hu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY