The potential for machine learning in hybrid QM/MM calculations.
暂无分享,去创建一个
Yin-Jia Zhang | Alireza Khorshidi | Georg Kastlunger | Andrew A Peterson | A. Peterson | A. Khorshidi | Yinjia Zhang | Georg Kastlunger | Georg Kastlunger
[1] J Behler,et al. Representing potential energy surfaces by high-dimensional neural network potentials , 2014, Journal of physics. Condensed matter : an Institute of Physics journal.
[2] Joan-Emma Shea,et al. Easy transition path sampling methods: flexible-length aimless shooting and permutation shooting. , 2015, Journal of chemical theory and computation.
[3] S. Klippenstein,et al. Long-range transition state theory. , 2005, The Journal of chemical physics.
[4] R. Marcus,et al. High pressure rate constants for unimolecular dissociation/free radical recombination: Determination of the quantum correction via quantum Monte Carlo path integration , 1987 .
[5] S. C. Rogers,et al. QUASI: A general purpose implementation of the QM/MM approach and its application to problems in catalysis , 2003 .
[6] S. Klippenstein. Variational optimizations in the Rice–Ramsperger–Kassel–Marcus theory calculations for unimolecular dissociations with no reverse barrier , 1992 .
[7] Stephen J. Klippenstein,et al. Variable reaction coordinate transition state theory: Analytic results and application to the C2H3+H→C2H4 reaction , 2003 .
[8] H. Jónsson,et al. Grid-Based Projector Augmented Wave (GPAW) Implementation of Quantum Mechanics/Molecular Mechanics (QM/MM) Electrostatic Embedding and Application to a Solvated Diplatinum Complex. , 2017, Journal of chemical theory and computation.
[9] W. Heisenberg,et al. Zur Quantentheorie der Molekeln , 1924 .
[10] Michele Parrinello,et al. Generalized neural-network representation of high-dimensional potential-energy surfaces. , 2007, Physical review letters.
[11] Steven D. Brown,et al. Neural network models of potential energy surfaces , 1995 .
[12] Hao Hu,et al. Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes. , 2009, Theochem.
[13] R. Swendsen,et al. THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method , 1992 .
[14] Alessandro De Vita,et al. A framework for machine‐learning‐augmented multiscale atomistic simulations on parallel supercomputers , 2015 .
[15] George E. Karniadakis,et al. An Atomistic Fingerprint Algorithm for Learning Ab Initio Molecular Force Fields , 2018, The Journal of chemical physics.
[16] Dominik Marx,et al. Nonadiabatic hybrid quantum and molecular mechanic simulations of azobenzene photoswitching in bulk liquid environment. , 2010, The journal of physical chemistry. A.
[17] Francesca Tavazza,et al. Considerations for choosing and using force fields and interatomic potentials in materials science and engineering , 2013 .
[18] K. Morokuma,et al. ONIOM: A Multilayered Integrated MO + MM Method for Geometry Optimizations and Single Point Energy Predictions. A Test for Diels−Alder Reactions and Pt(P(t-Bu)3)2 + H2 Oxidative Addition , 1996 .
[19] B. C. Garrett,et al. Current status of transition-state theory , 1983 .
[20] K. Morokuma,et al. A NEW ONIOM IMPLEMENTATION IN GAUSSIAN98. PART I. THE CALCULATION OF ENERGIES, GRADIENTS, VIBRATIONAL FREQUENCIES AND ELECTRIC FIELD DERIVATIVES , 1999 .
[21] M. Baskes,et al. Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals , 1984 .
[22] Karsten W. Jacobsen,et al. An object-oriented scripting interface to a legacy electronic structure code , 2002, Comput. Sci. Eng..
[23] Basile F. E. Curchod,et al. Nonadiabatic molecular dynamics with solvent effects: A LR-TDDFT QM/MM study of ruthenium (II) tris (bipyridine) in water , 2011 .
[24] Nobuyuki Matubayasi,et al. A quantum chemical approach to the free energy calculations in condensed systems: the QM/MM method combined with the theory of energy representation. , 2004, The Journal of chemical physics.
[25] Matthew G. Quesne,et al. QM and QM/MM Methods Compared: Case Studies on Reaction Mechanisms of Metalloenzymes. , 2015, Advances in protein chemistry and structural biology.
[26] Zhenwei Li,et al. Molecular dynamics with on-the-fly machine learning of quantum-mechanical forces. , 2015, Physical review letters.
[27] M. Karplus,et al. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations , 1990 .
[28] P. Popelier,et al. Potential energy surfaces fitted by artificial neural networks. , 2010, The journal of physical chemistry. A.
[29] R. Friesner,et al. Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis. , 2005, Annual review of physical chemistry.
[30] M. Levitt,et al. Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. , 1976, Journal of molecular biology.
[31] Donald G Truhlar,et al. Modeling the kinetics of bimolecular reactions. , 2006, Chemical reviews.
[32] Shina Caroline Lynn Kamerlin,et al. Recent advances in QM/MM free energy calculations using reference potentials☆ , 2015, Biochimica et biophysica acta.
[33] D. Truhlar,et al. QM/MM: what have we learned, where are we, and where do we go from here? , 2007 .
[34] William A. Curtin,et al. Multiscale quantum/atomistic coupling using constrained density functional theory , 2013 .
[35] Rampi Ramprasad,et al. Learning scheme to predict atomic forces and accelerate materials simulations , 2015, 1505.02701.
[36] Francesca Tavazza,et al. Facilitating the selection and creation of accurate interatomic potentials with robust tools and characterization , 2015 .
[37] J. Dayhoff,et al. Artificial neural networks , 2001, Cancer.
[38] Vivek B Shenoy,et al. Anomalous Strength Characteristics of Tilt Grain Boundaries in Graphene , 2010, Science.
[39] Lee‐Ping Wang,et al. A Polarizable QM/MM Explicit Solvent Model for Computational Electrochemistry in Water. , 2012, Journal of chemical theory and computation.
[40] Hai Lin,et al. Adaptive quantum/molecular mechanics: what have we learned, where are we, and where do we go from here? , 2017 .
[41] J. Behler. Perspective: Machine learning potentials for atomistic simulations. , 2016, The Journal of chemical physics.
[42] A. Laio,et al. Escaping free-energy minima , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[43] Walter Thiel,et al. Nobel 2013 Chemistry: Methods for computational chemistry , 2013, Nature.
[44] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[45] G. Torrie,et al. Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling , 1977 .
[46] Walter Thiel,et al. QM/MM methods for biomolecular systems. , 2009, Angewandte Chemie.
[47] Stefan Goedecker,et al. Interatomic potentials for ionic systems with density functional accuracy based on charge densities obtained by a neural network , 2015, 1501.07344.
[48] Peter G. Boyd,et al. Force-Field Prediction of Materials Properties in Metal-Organic Frameworks , 2016, The journal of physical chemistry letters.
[49] Alireza Khorshidi,et al. Amp: A modular approach to machine learning in atomistic simulations , 2016, Comput. Phys. Commun..
[50] Sudhir B. Kylasa,et al. The ReaxFF reactive force-field: development, applications and future directions , 2016 .
[51] U. Singh,et al. A NEW FORCE FIELD FOR MOLECULAR MECHANICAL SIMULATION OF NUCLEIC ACIDS AND PROTEINS , 1984 .
[52] J. Andrew McCammon,et al. Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units , 2013, Journal of chemical theory and computation.
[53] Alfredo Caro,et al. Grain-boundary structures in polycrystalline metals at the nanoscale , 2000 .
[54] David Chandler,et al. Transition path sampling: throwing ropes over rough mountain passes, in the dark. , 2002, Annual review of physical chemistry.
[55] Yi Liu,et al. An improved QM/MM approach for metals , 2007 .
[56] S. Klippenstein. AN EFFICIENT PROCEDURE FOR EVALUATING THE NUMBER OF AVAILABLE STATES WITHIN A VARIABLY DEFINED REACTION COORDINATE FRAMEWORK , 1994 .
[57] Stephen J. Klippenstein,et al. Transition State Theory for Multichannel Addition Reactions: Multifaceted Dividing Surfaces , 2003 .
[58] Itamar Borges,et al. Water solvent effects using continuum and discrete models: The nitromethane molecule, CH3NO2 , 2015, J. Comput. Chem..
[59] W. L. Jorgensen,et al. The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. , 1988, Journal of the American Chemical Society.
[60] Jacob Kongsted,et al. Excited States in Solution through Polarizable Embedding , 2010 .
[61] Wright,et al. Density-functional calculations for grain boundaries in aluminum. , 1994, Physical review. B, Condensed matter.
[62] L. Nilsson,et al. Structure and Dynamics of the TIP3P, SPC, and SPC/E Water Models at 298 K , 2001 .
[63] M. W. van der Kamp,et al. Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology. , 2013, Biochemistry.
[64] Blazej Grabowski,et al. A QM/MM approach for low-symmetry defects in metals , 2016 .
[65] D. Goldfarb. A family of variable-metric methods derived by variational means , 1970 .
[66] Lawrence B. Harding,et al. A Direct Transition State Theory Based Study of Methyl Radical Recombination Kinetics , 1999 .
[67] R. Kondor,et al. Gaussian approximation potentials: the accuracy of quantum mechanics, without the electrons. , 2009, Physical review letters.
[68] Eduardo M. Sproviero,et al. Deposition of an oxomanganese water oxidation catalyst on TiO2 nanoparticles: computational modeling, assembly and characterization , 2009 .
[69] Cheng Lu,et al. Atomistic Simulation of Tensile Deformation Behavior of ∑5 Tilt Grain Boundaries in Copper Bicrystal , 2014, Scientific Reports.
[70] Min Zheng,et al. Adaptive quantum mechanics/molecular mechanics methods , 2016 .
[71] David Chandler,et al. Statistical mechanics of isomerization dynamics in liquids and the transition state approximation , 1978 .
[72] Kamal Choudhary,et al. Evaluation and comparison of classical interatomic potentials through a user-friendly interactive web-interface , 2017, Scientific Data.
[73] Johan A. K. Suykens,et al. Least Squares Support Vector Machine Classifiers , 1999, Neural Processing Letters.
[74] J. Kästner. Umbrella sampling , 2011 .
[75] Markus Meuwly,et al. Modelling Chemical Reactions Using Empirical Force Fields , 2017 .
[76] M. Parrinello,et al. Well-tempered metadynamics: a smoothly converging and tunable free-energy method. , 2008, Physical review letters.
[77] Donald G Truhlar,et al. Adaptive partitioning in combined quantum mechanical and molecular mechanical calculations of potential energy functions for multiscale simulations. , 2007, The journal of physical chemistry. B.
[78] B. Trout,et al. Obtaining reaction coordinates by likelihood maximization. , 2006, The Journal of chemical physics.
[79] Aron Walsh,et al. A general forcefield for accurate phonon properties of metal-organic frameworks. , 2016, Physical chemistry chemical physics : PCCP.
[80] E Weinan,et al. Multiscale simulations in simple metals: A density-functional-based methodology , 2004, cond-mat/0404414.
[81] Timothy C. Berkelbach,et al. Grains and grain boundaries in highly crystalline monolayer molybdenum disulphide. , 2013, Nature Materials.
[82] Weitao Yang,et al. Challenges for density functional theory. , 2012, Chemical reviews.
[83] J. Stephen. The evaluation of NE(R) within a variably defined reaction coordinate framework , 1993 .
[84] Louis Vanduyfhuys,et al. Extension of the QuickFF force field protocol for an improved accuracy of structural, vibrational, mechanical and thermal properties of metal–organic frameworks , 2018, J. Comput. Chem..
[85] W. D. Allen,et al. A high level ab initio map and direct statistical treatment of the fragmentation of singlet ketene , 1996 .
[86] Alireza Khorshidi,et al. Addressing uncertainty in atomistic machine learning. , 2017, Physical chemistry chemical physics : PCCP.
[87] Shoushan Fan,et al. Grain-boundary-dependent CO2 electroreduction activity. , 2015, Journal of the American Chemical Society.
[88] Nongnuch Artrith,et al. High-dimensional neural-network potentials for multicomponent systems: Applications to zinc oxide , 2011 .
[89] William A. Goddard,et al. The Hessian biased force field for silicon nitride ceramics: Predictions of thermodynamic and mechanical properties for α‐ and β‐Si3N4 , 1992 .
[90] Andrew A Peterson,et al. Acceleration of saddle-point searches with machine learning. , 2016, The Journal of chemical physics.
[91] Reinhard Klein,et al. Shape retrieval using 3D Zernike descriptors , 2004, Comput. Aided Des..