Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks
暂无分享,去创建一个
[1] Alexander D. MacKerell,et al. Polarizable Force Field for DNA Based on the Classical Drude Oscillator: II. Microsecond Molecular Dynamics Simulations of Duplex DNA. , 2017, Journal of chemical theory and computation.
[2] Alexander D. MacKerell. Empirical force fields for biological macromolecules: Overview and issues , 2004, J. Comput. Chem..
[3] Alexander D. MacKerell,et al. Induction of peptide bond dipoles drives cooperative helix formation in the (AAQAA)3 peptide. , 2014, Biophysical journal.
[4] H R Drew,et al. Structure of a B-DNA dodecamer: conformation and dynamics. , 1981, Proceedings of the National Academy of Sciences of the United States of America.
[5] Alexander D. MacKerell,et al. Polarizable Empirical Force Field for Halogen-Containing Compounds Based on the Classical Drude Oscillator. , 2018, Journal of chemical theory and computation.
[6] S. Nosé. A unified formulation of the constant temperature molecular dynamics methods , 1984 .
[7] Diwakar Shukla,et al. OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation. , 2013, Journal of chemical theory and computation.
[8] Klaus Schulten,et al. High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD. , 2011, The journal of physical chemistry letters.
[9] Laxmikant V. Kalé,et al. Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..
[10] Alexander D. MacKerell,et al. Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field. , 2013, Faraday discussions.
[11] B. Thole. Molecular polarizabilities calculated with a modified dipole interaction , 1981 .
[12] Ity Sharma,et al. Using polarizable POSSIM force field and fuzzy‐border continuum solvent model to calculate pKa shifts of protein residues , 2017, J. Comput. Chem..
[13] J. Crain,et al. Quantum Drude oscillator model of atoms and molecules: many-body polarization and dispersion interactions for atomistic simulation. , 2013 .
[14] Alexander D. MacKerell,et al. A polarizable model of water for molecular dynamics simulations of biomolecules , 2006 .
[15] C. R. Mann. The Theory of Optics , 1903, Nature.
[16] George A. Kaminski,et al. Polarizable Simulations with Second order Interaction Model - force field and software for fast polarizable calculations: Parameters for small model systems and free energy calculations. , 2009, Journal of chemical theory and computation.
[17] Hoover,et al. Canonical dynamics: Equilibrium phase-space distributions. , 1985, Physical review. A, General physics.
[18] Piotr Cieplak,et al. Polarization effects in molecular mechanical force fields , 2009, Journal of physics. Condensed matter : an Institute of Physics journal.
[19] Alexander D. MacKerell,et al. Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field. , 2010, Journal of chemical theory and computation.
[20] Berk Hess,et al. Improving efficiency of large time‐scale molecular dynamics simulations of hydrogen‐rich systems , 1999, Journal of computational chemistry.
[21] Alexander D. MacKerell,et al. CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model , 2004, J. Comput. Chem..
[22] Alexander D. MacKerell,et al. Balancing the Interactions of Mg2+ in Aqueous Solution and with Nucleic Acid Moieties For a Polarizable Force Field Based on the Classical Drude Oscillator Model. , 2016, The journal of physical chemistry. B.
[23] Berk Hess,et al. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers , 2015 .
[24] Benoît Roux,et al. A polarizable force field of dipalmitoylphosphatidylcholine based on the classical Drude model for molecular dynamics simulations of lipids. , 2013, The journal of physical chemistry. B.
[25] Benoît Roux,et al. Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm , 2003 .
[26] Zhi Wang,et al. Tinker‐OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs , 2017, J. Comput. Chem..
[27] T. Darden,et al. Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .
[28] Margaret E. Johnson,et al. Current status of the AMOEBA polarizable force field. , 2010, The journal of physical chemistry. B.
[29] Jianpeng Ma,et al. CHARMM: The biomolecular simulation program , 2009, J. Comput. Chem..
[30] Glenn J. Martyna,et al. A unified formalism for many-body polarization and dispersion: The quantum Drude model applied to fluid xenon , 2006 .
[31] Alexander D. MacKerell,et al. CHARMM additive and polarizable force fields for biophysics and computer-aided drug design. , 2015, Biochimica et biophysica acta.
[32] Benoît Roux,et al. Atomic Level Anisotropy in the Electrostatic Modeling of Lone Pairs for a Polarizable Force Field Based on the Classical Drude Oscillator. , 2006, Journal of chemical theory and computation.
[33] Ruhong Zhou,et al. Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model , 1999 .
[34] Alexander D. MacKerell,et al. Force Field for Peptides and Proteins based on the Classical Drude Oscillator. , 2013, Journal of chemical theory and computation.
[35] Pengyu Y. Ren,et al. The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins. , 2013, Journal of chemical theory and computation.
[36] A. Roitberg,et al. Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning. , 2015, Journal of chemical theory and computation.
[37] Alexander D. MacKerell,et al. An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications , 2016, Chemical reviews.
[38] Charles L. Brooks,et al. CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations , 2004, J. Comput. Chem..
[39] Michael R Shirts,et al. Simple Quantitative Tests to Validate Sampling from Thermodynamic Ensembles. , 2012, Journal of chemical theory and computation.
[40] C. Bugg,et al. Structure of ubiquitin refined at 1.8 A resolution. , 1987, Journal of molecular biology.
[41] Alexander D. MacKerell,et al. Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model , 2015, J. Comput. Chem..
[42] L. B. Perry,et al. Influence of Anesthetic Agent on Response to Hemorrhagic Hypotension , 1974, Anesthesiology.
[43] T. Darden,et al. A smooth particle mesh Ewald method , 1995 .
[44] Alexander D. MacKerell,et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.