Forces are not Enough: Benchmark and Critical Evaluation for Machine Learning Force Fields with Molecular Simulations
暂无分享,去创建一个
[1] Johannes T. Margraf,et al. How robust are modern graph neural network potentials in long and hot molecular dynamics simulations? , 2022, Mach. Learn. Sci. Technol..
[2] Benjamin P. Pritchard,et al. SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials , 2022, Scientific Data.
[3] Wujie Wang,et al. Learning Pair Potentials using Differentiable Simulations , 2022, The Journal of chemical physics.
[4] A. Tkatchenko,et al. Towards Linearly Scaling and Chemically Accurate Global Machine Learning Force Fields for Large Molecules , 2022, 2209.03985.
[5] Yi Liao,et al. Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs , 2022, ICLR.
[6] Zachary W. Ulissi,et al. The Open Catalyst 2022 (OC22) Dataset and Challenges for Oxide Electrocatalysis , 2022, ACS Catalysis.
[7] Zachary W. Ulissi,et al. Open Challenges in Developing Generalizable Large-Scale Machine-Learning Models for Catalyst Discovery , 2022, ACS Catalysis.
[8] Simon L. Batzner,et al. The Design Space of E(3)-Equivariant Atom-Centered Interatomic Potentials , 2022, ArXiv.
[9] Simon L. Batzner,et al. Learning local equivariant representations for large-scale atomistic dynamics , 2022, Nature Communications.
[10] Zachary W. Ulissi,et al. GemNet-OC: Developing Graph Neural Networks for Large and Diverse Molecular Simulation Datasets , 2022, Trans. Mach. Learn. Res..
[11] Oliver T. Unke,et al. Automatic identification of chemical moieties , 2022, Physical chemistry chemical physics : PCCP.
[12] Chi Chen,et al. A universal graph deep learning interatomic potential for the periodic table , 2022, Nature Computational Science.
[13] Cas van der Oord,et al. Linear Atomic Cluster Expansion Force Fields for Organic Molecules: Beyond RMSE , 2021, Journal of chemical theory and computation.
[14] Gábor Csányi,et al. Linear Atomic Cluster Expansion Force Fields for Organic Molecules: beyond RMSE , 2021 .
[15] Toshiki Kataoka,et al. Towards universal neural network potential for material discovery applicable to arbitrary combination of 45 elements , 2021, Nature Communications.
[16] P. Battaglia,et al. Simple GNN Regularisation for 3D Molecular Property Prediction&Beyond , 2021, 2106.07971.
[17] Cecilia Clementi,et al. Machine learning implicit solvation for molecular dynamics. , 2021, The Journal of chemical physics.
[18] Florian Becker,et al. GemNet: Universal Directional Graph Neural Networks for Molecules , 2021, NeurIPS.
[19] Julija Zavadlav,et al. Learning neural network potentials from experimental data via Differentiable Trajectory Reweighting , 2021, Nature Communications.
[20] Jonathan P. Mailoa,et al. Accurate and scalable graph neural network force field and molecular dynamics with direct force architecture , 2021, npj Computational Materials.
[21] Klaus-Robert Müller,et al. SpookyNet: Learning force fields with electronic degrees of freedom and nonlocal effects , 2021, Nature Communications.
[22] Justin S. Smith,et al. Modeling of Peptides with Classical and Novel Machine Learning Force Fields: A Comparison. , 2021, The journal of physical chemistry. B.
[23] J. Leskovec,et al. ForceNet: A Graph Neural Network for Large-Scale Quantum Calculations , 2021, ArXiv.
[24] Max Welling,et al. E(n) Equivariant Graph Neural Networks , 2021, ICML.
[25] Joe G Greener,et al. Differentiable molecular simulation can learn all the parameters in a coarse-grained force field for proteins , 2021, bioRxiv.
[26] Michael Gastegger,et al. Equivariant message passing for the prediction of tensorial properties and molecular spectra , 2021, ICML.
[27] Rafael Gómez-Bombarelli,et al. Differentiable sampling of molecular geometries with uncertainty-based adversarial attacks , 2021, Nature Communications.
[28] R. Car,et al. When do short-range atomistic machine-learning models fall short? , 2021, The Journal of chemical physics.
[29] Jeremiah A. Johnson,et al. Accelerating amorphous polymer electrolyte screening by learning to reduce errors in molecular dynamics simulated properties , 2021, Nature Communications.
[30] Jonathan P. Mailoa,et al. E(3)-equivariant graph neural networks for data-efficient and accurate interatomic potentials , 2021, Nature Communications.
[31] Toni Giorgino,et al. TorchMD: A Deep Learning Framework for Molecular Simulations , 2020, Journal of chemical theory and computation.
[32] E. D. Cubuk,et al. JAX, M.D. A framework for differentiable physics , 2020, NeurIPS.
[33] Weihua Hu,et al. The Open Catalyst 2020 (OC20) Dataset and Community Challenges , 2020, ACS Catalysis.
[34] Michael Gastegger,et al. Machine Learning Force Fields , 2020, Chemical reviews.
[35] A. Tkatchenko,et al. QM7-X: A comprehensive dataset of quantum-mechanical properties spanning the chemical space of small organic molecules , 2020, 2006.15139.
[36] Wujie Wang,et al. Active learning and neural network potentials accelerate molecular screening of ether-based solvate ionic liquids. , 2020, Chemical communications.
[37] Stephan Günnemann,et al. Directional Message Passing for Molecular Graphs , 2020, ICLR.
[38] Andrew L. Ferguson,et al. Machine learning for collective variable discovery and enhanced sampling in biomolecular simulation , 2020, Molecular Physics.
[39] Wujie Wang,et al. Differentiable Molecular Simulations for Control and Learning , 2020, ArXiv.
[40] Jure Leskovec,et al. Learning to Simulate Complex Physics with Graph Networks , 2020, ICML.
[41] Patrick La Riviere,et al. Transforming the development and dissemination of cutting-edge microscopy and computation , 2019, Nature Methods.
[42] Junmei Wang,et al. End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design. , 2019, Chemical reviews.
[43] Simon L. Batzner,et al. On-the-fly active learning of interpretable Bayesian force fields for atomistic rare events , 2019, npj Computational Materials.
[44] Wujie Wang,et al. Coarse-graining auto-encoders for molecular dynamics , 2018, npj Computational Materials.
[45] Frank Noé,et al. Machine Learning of Coarse-Grained Molecular Dynamics Force Fields , 2018, ACS central science.
[46] Debora S. Marks,et al. Learning Protein Structure with a Differentiable Simulator , 2018, ICLR.
[47] E Weinan,et al. End-to-end Symmetry Preserving Inter-atomic Potential Energy Model for Finite and Extended Systems , 2018, NeurIPS.
[48] Markus Meuwly,et al. A reactive, scalable, and transferable model for molecular energies from a neural network approach based on local information. , 2018, The Journal of chemical physics.
[49] Li Li,et al. Tensor Field Networks: Rotation- and Translation-Equivariant Neural Networks for 3D Point Clouds , 2018, ArXiv.
[50] Mohammad M. Sultan,et al. Transferable Neural Networks for Enhanced Sampling of Protein Dynamics. , 2018, Journal of chemical theory and computation.
[51] Mark E Tuckerman,et al. Stochastic Neural Network Approach for Learning High-Dimensional Free Energy Surfaces. , 2017, Physical review letters.
[52] George E. Dahl,et al. Prediction Errors of Molecular Machine Learning Models Lower than Hybrid DFT Error. , 2017, Journal of chemical theory and computation.
[53] E Weinan,et al. Deep Potential Molecular Dynamics: a scalable model with the accuracy of quantum mechanics , 2017, Physical review letters.
[54] Michael Walter,et al. The atomic simulation environment-a Python library for working with atoms. , 2017, Journal of physics. Condensed matter : an Institute of Physics journal.
[55] Klaus-Robert Müller,et al. SchNet: A continuous-filter convolutional neural network for modeling quantum interactions , 2017, NIPS.
[56] Gerbrand Ceder,et al. Efficient and accurate machine-learning interpolation of atomic energies in compositions with many species , 2017, 1706.06293.
[57] Samuel S. Schoenholz,et al. Neural Message Passing for Quantum Chemistry , 2017, ICML.
[58] Vijay S. Pande,et al. OpenMM 7: Rapid development of high performance algorithms for molecular dynamics , 2016, bioRxiv.
[59] Klaus-Robert Müller,et al. Machine learning of accurate energy-conserving molecular force fields , 2016, Science Advances.
[60] Alireza Khorshidi,et al. Amp: A modular approach to machine learning in atomistic simulations , 2016, Comput. Phys. Commun..
[61] Berk Hess,et al. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers , 2015 .
[62] Brett M. Savoie,et al. Systematic Computational and Experimental Investigation of Lithium-Ion Transport Mechanisms in Polyester-Based Polymer Electrolytes , 2015, ACS central science.
[63] Pavlo O. Dral,et al. Quantum chemistry structures and properties of 134 kilo molecules , 2014, Scientific Data.
[64] Massimiliano Bonomi,et al. PLUMED 2: New feathers for an old bird , 2013, Comput. Phys. Commun..
[65] Kyle A. Beauchamp,et al. Markov state model reveals folding and functional dynamics in ultra-long MD trajectories. , 2011, Journal of the American Chemical Society.
[66] R. Dror,et al. How Fast-Folding Proteins Fold , 2011, Science.
[67] M. Tuckerman. Statistical Mechanics: Theory and Molecular Simulation , 2010 .
[68] Charles L. Brooks,et al. A theoretical study of alanine dipeptide and analogs , 2009 .
[69] M. Feig. Kinetics from Implicit Solvent Simulations of Biomolecules as a Function of Viscosity. , 2007, Journal of chemical theory and computation.
[70] Michele Parrinello,et al. Generalized neural-network representation of high-dimensional potential-energy surfaces. , 2007, Physical review letters.
[71] G. Voth,et al. Flexible simple point-charge water model with improved liquid-state properties. , 2006, The Journal of chemical physics.
[72] Julian Tirado-Rives,et al. Potential energy functions for atomic-level simulations of water and organic and biomolecular systems. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[73] A. Laio,et al. Escaping free-energy minima , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[74] R. Friesner,et al. Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides† , 2001 .
[75] Berend Smit,et al. Understanding molecular simulation: from algorithms to applications , 1996 .
[76] T. Halgren. Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94 , 1996, J. Comput. Chem..
[77] P. Kollman,et al. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .
[78] Adriano Filipponi,et al. The radial distribution function probed by X-ray absorption spectroscopy , 1994 .
[79] Mark E. Tuckerman,et al. Reversible multiple time scale molecular dynamics , 1992 .
[80] R. L. Henderson. A uniqueness theorem for fluid pair correlation functions , 1974 .
[81] R. G. Wenzel,et al. Structure Factor and Radial Distribution Function for Liquid Argon at 85 °K , 1973 .
[82] Aneesur Rahman,et al. Correlations in the Motion of Atoms in Liquid Argon , 1964 .
[83] B. Alder,et al. Studies in Molecular Dynamics. I. General Method , 1959 .
[84] M. Welling,et al. Path Integral Stochastic Optimal Control for Sampling Transition Paths , 2022, ArXiv.
[85] G. D. Fabritiis,et al. TorchMD-NET: Equivariant Transformers for Neural Network based Molecular Potentials , 2022, ICLR.
[86] Nathan J. Rebello,et al. Simulate Time-integrated Coarse-grained Molecular Dynamics with Geometric Machine Learning , 2022, ArXiv.
[87] S. Ji,et al. Spherical Message Passing for 3D Molecular Graphs , 2022, ICLR.
[88] Thomas F. Miller,et al. UNiTE: Unitary N-body Tensor Equivariant Network with Applications to Quantum Chemistry , 2021, ArXiv.
[89] O. Isayev,et al. ANI-1: an extensible neural network potential with DFT accuracy at force fi eld computational cost † , 2017 .
[90] J. Ponder,et al. Force fields for protein simulations. , 2003, Advances in protein chemistry.
[91] J. Crabbe,et al. Molecular modelling: Principles and applications , 1997 .
[92] D. W. Noid. Studies in Molecular Dynamics , 1976 .