Multiple Time-Step Dual-Hamiltonian Hybrid Molecular Dynamics - Monte Carlo Canonical Propagation Algorithm.
暂无分享,去创建一个
Jonathan Weare | Yunjie Chen | Benoît Roux | Seyit Kale | Aaron R. Dinner | B. Roux | A. Dinner | Seyit Kale | Yunjie Chen | J. Weare
[1] Efficient hybrid non-equilibrium molecular dynamics--Monte Carlo simulations with symmetric momentum reversal. , 2014, The Journal of chemical physics.
[2] Jesús A. Izaguirre,et al. Nonlinear instability in multiple time stepping molecular dynamics , 2003, SAC '03.
[3] Alexander D. MacKerell,et al. Computational Biochemistry and Biophysics , 2001 .
[4] H. Stern. Molecular simulation with variable protonation states at constant pH. , 2007, The Journal of chemical physics.
[5] David D L Minh,et al. Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation , 2011, Proceedings of the National Academy of Sciences.
[6] Y. Maday,et al. A parareal in time procedure for the control of partial differential equations , 2002 .
[7] J. Pople,et al. Self—Consistent Molecular Orbital Methods. XII. Further Extensions of Gaussian—Type Basis Sets for Use in Molecular Orbital Studies of Organic Molecules , 1972 .
[8] Philip Heidelberger,et al. A spectral method for confidence interval generation and run length control in simulations , 1981, CACM.
[9] Jesús A. Izaguirre,et al. The Five Femtosecond Time Step Barrier , 1999, Computational Molecular Dynamics.
[10] Edward D Harder,et al. Efficient multiple time step method for use with Ewald and particle mesh Ewald for large biomolecular systems , 2001 .
[11] P. C. Hariharan,et al. The influence of polarization functions on molecular orbital hydrogenation energies , 1973 .
[12] Sebastian Reich,et al. Multiple-time-stepping generalized hybrid Monte Carlo methods , 2015, J. Comput. Phys..
[13] M. Tuckerman,et al. Long time molecular dynamics for enhanced conformational sampling in biomolecular systems. , 2004, Physical review letters.
[14] H. Trotter. On the product of semi-groups of operators , 1959 .
[15] V. Pande,et al. Normal mode partitioning of Langevin dynamics for biomolecules. , 2008, The Journal of chemical physics.
[16] Sebastian Reich,et al. GSHMC: An efficient method for molecular simulation , 2008, J. Comput. Phys..
[17] M. Tuckerman,et al. A Liouville-operator derived measure-preserving integrator for molecular dynamics simulations in the isothermal–isobaric ensemble , 2006 .
[18] J. Stewart. Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements , 2007, Journal of molecular modeling.
[19] Joost VandeVondele,et al. Ab initio molecular dynamics using hybrid density functionals. , 2008, The Journal of chemical physics.
[20] B. Roux,et al. Generalized Metropolis acceptance criterion for hybrid non-equilibrium molecular dynamics-Monte Carlo simulations. , 2015, The Journal of chemical physics.
[21] T. Schlick,et al. Efficient multiple-time-step integrators with distance-based force splitting for particle-mesh-Ewald molecular dynamics simulations , 2002 .
[22] N. Metropolis,et al. Equation of State Calculations by Fast Computing Machines , 1953, Resonance.
[23] Christina Gloeckner,et al. Modern Applied Statistics With S , 2003 .
[24] E. Carter,et al. Time-Reversible Multiple Time Scale ab Initio Molecular Dynamics , 1993 .
[25] B. Berne,et al. Multiple "time step" Monte Carlo , 2002 .
[26] B. Leimkuhler,et al. Robust and efficient configurational molecular sampling via Langevin dynamics. , 2013, The Journal of chemical physics.
[27] M. Parrinello,et al. Canonical sampling through velocity rescaling. , 2007, The Journal of chemical physics.
[28] R. Tweedie,et al. Geometric convergence and central limit theorems for multidimensional Hastings and Metropolis algorithms , 1996 .
[29] Walter Thiel,et al. Machine Learning of Parameters for Accurate Semiempirical Quantum Chemical Calculations , 2015, Journal of chemical theory and computation.
[30] J. Izaguirre. Longer Time Steps for Molecular Dynamics , 1999 .
[31] Zhenwei Li,et al. Molecular dynamics with on-the-fly machine learning of quantum-mechanical forces. , 2015, Physical review letters.
[32] T. Schlick,et al. Overcoming stability limitations in biomolecular dynamics. I. Combining force splitting via extrapolation with Langevin dynamics in LN , 1998 .
[33] Stefan Goedecker,et al. Extending molecular simulation time scales : Parallel in time integrations for high-level quantum chemistry and complex force representations , 2014 .
[34] Mark E. Tuckerman,et al. Explicit reversible integrators for extended systems dynamics , 1996 .
[35] John D. Chodera,et al. Time Step Rescaling Recovers Continuous-Time Dynamical Properties for Discrete-Time Langevin Integration of Nonequilibrium Systems , 2013, The journal of physical chemistry. B.
[36] B. Leimkuhler,et al. Molecular Dynamics: With Deterministic and Stochastic Numerical Methods , 2015 .
[37] E. Vanden-Eijnden,et al. Pathwise accuracy and ergodicity of metropolized integrators for SDEs , 2009, 0905.4218.
[38] Richard A. Davis,et al. Time Series: Theory and Methods , 2013 .
[39] Efficient mixed-force first-principles molecular dynamics. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.
[40] Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics—Monte Carlo Simulations Guided by a Coarse-Grained Model , 2015, Journal of chemical theory and computation.
[41] Andrew J Ballard,et al. Replica exchange with nonequilibrium switches , 2009, Proceedings of the National Academy of Sciences.
[42] John D. Chodera,et al. Using Nonequilibrium Fluctuation Theorems to Understand and Correct Errors in Equilibrium and Nonequ , 2011, 1107.2967.
[43] Klaus Schulten,et al. Generalized Verlet Algorithm for Efficient Molecular Dynamics Simulations with Long-range Interactions , 1991 .
[44] B. Brooks,et al. An analysis of the accuracy of Langevin and molecular dynamics algorithms , 1988 .
[45] B. Roux,et al. Constant-pH Hybrid Nonequilibrium Molecular Dynamics–Monte Carlo Simulation Method , 2015, Journal of chemical theory and computation.
[46] Ryan P Steele,et al. Communication: Multiple-timestep ab initio molecular dynamics with electron correlation. , 2013, The Journal of chemical physics.
[47] Alfredo Mayall Simas,et al. RM1: A reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I , 2006, J. Comput. Chem..
[48] Mark E. Tuckerman,et al. Molecular dynamics algorithm for multiple time scales: Systems with long range forces , 1991 .
[49] A. Alexandrova,et al. AFFCK: Adaptive Force-Field-Assisted ab Initio Coalescence Kick Method for Global Minimum Search. , 2015, Journal of chemical theory and computation.
[50] M. Tuckerman. Statistical Mechanics: Theory and Molecular Simulation , 2010 .
[51] M. Karplus,et al. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations , 1990 .
[52] S. Xantheas,et al. The binding energies of the D2d and S4 water octamer isomers: high-level electronic structure and empirical potential results. , 2004, Journal of Chemical Physics.
[53] Robert D. Skeel,et al. Long-Time-Step Methods for Oscillatory Differential Equations , 1998, SIAM J. Sci. Comput..
[54] C. Brooks. Computer simulation of liquids , 1989 .
[55] Thomas E Markland,et al. Multiple time step integrators in ab initio molecular dynamics. , 2014, The Journal of chemical physics.
[56] T. H. Dunning. Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen , 1989 .
[57] G. Strang. On the Construction and Comparison of Difference Schemes , 1968 .
[58] Aaron R. Dinner,et al. Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol , 2014, Journal of chemical theory and computation.
[59] R. Skeel,et al. Langevin stabilization of molecular dynamics , 2001 .
[60] Bo Qi,et al. Using multiscale preconditioning to accelerate the convergence of iterative molecular calculations. , 2014, The Journal of chemical physics.
[61] Mark E. Tuckerman,et al. Reversible multiple time scale molecular dynamics , 1992 .
[62] B. Leimkuhler,et al. Stochastic, resonance-free multiple time-step algorithm for molecular dynamics with very large time steps , 2013, 1307.1167.
[63] A. Becke. Density-functional thermochemistry. III. The role of exact exchange , 1993 .
[64] Benedict Leimkuhler,et al. Computational Molecular Dynamics: Challenges, Methods, Ideas , 1999, Computational Molecular Dynamics.
[65] C. Dellago,et al. Equilibrium free energies from fast-switching trajectories with large time steps. , 2005, The Journal of chemical physics.