Nonequilibrium candidate Monte Carlo: A new tool for efficient equilibrium simulation

A new tool for efficient equilibrium simulation Jerome P. Nilmeier ∗, Gavin E. Crooks †, David D. L. Minh ‡, and John D. Chodera § ∗Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA,†Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA,‡Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, USA, and §California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, USA

[1]  Gabriel Stoltz,et al.  Langevin dynamics with constraints and computation of free energy differences , 2010, Math. Comput..

[2]  T. Lelièvre,et al.  Free Energy Computations: A Mathematical Perspective , 2010 .

[3]  Tamar Schlick,et al.  Molecular Modeling and Simulation: An Interdisciplinary Guide , 2010 .

[4]  Vijay S. Pande,et al.  OpenMM: A Hardware-Independent Framework for Molecular Simulations , 2010, Computing in Science & Engineering.

[5]  A. Doucet,et al.  Particle Markov chain Monte Carlo methods , 2010 .

[6]  Manuel Athènes,et al.  Free energy reconstruction from steered dynamics without post-processing , 2010, J. Comput. Phys..

[7]  Vijay S. Pande,et al.  Efficient nonbonded interactions for molecular dynamics on a graphics processing unit , 2010, J. Comput. Chem..

[8]  Jesús A. Izaguirre,et al.  Multiscale Dynamics of Macromolecules Using Normal Mode Langevin , 2010, Pacific Symposium on Biocomputing.

[9]  Michael P Eastwood,et al.  Minimizing thermodynamic length to select intermediate states for free-energy calculations and replica-exchange simulations. , 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.

[10]  S. Cheong,et al.  Stochastic boundary conditions for molecular dynamics simulations , 2009, 0910.1401.

[11]  Jerome Nilmeier,et al.  Monte Carlo Sampling with Hierarchical Move Sets: POSH Monte Carlo. , 2009, Journal of chemical theory and computation.

[12]  Andrew J Ballard,et al.  Replica exchange with nonequilibrium switches , 2009, Proceedings of the National Academy of Sciences.

[13]  David D. L. Minh,et al.  Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages. , 2009, The Journal of chemical physics.

[14]  Vijay S. Pande,et al.  Accelerating molecular dynamic simulation on graphics processing units , 2009, J. Comput. Chem..

[15]  Gavin E Crooks,et al.  Far-from-equilibrium measurements of thermodynamic length. , 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

[16]  Udo Seifert,et al.  Optimal protocols for minimal work processes in underdamped stochastic thermodynamics. , 2008, The Journal of chemical physics.

[17]  David D L Minh,et al.  Optimized free energies from bidirectional single-molecule force spectroscopy. , 2008, Physical review letters.

[18]  Michael R. Shirts,et al.  Statistically optimal analysis of samples from multiple equilibrium states. , 2008, The Journal of chemical physics.

[19]  A. Engel,et al.  Computing the optimal protocol for finite-time processes in stochastic thermodynamics. , 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

[20]  Sanghyun Park,et al.  Comparison of the serial and parallel algorithms of generalized ensemble simulations: an analytical approach. , 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

[21]  Gavin E Crooks,et al.  Measuring thermodynamic length. , 2007, Physical review letters.

[22]  H. Stern Molecular simulation with variable protonation states at constant pH. , 2007, The Journal of chemical physics.

[23]  U. Seifert,et al.  Optimal finite-time processes in stochastic thermodynamics. , 2007, Physical review letters.

[24]  Wei Yang,et al.  Simulated scaling method for localized enhanced sampling and simultaneous "alchemical" free energy simulations: a general method for molecular mechanical, quantum mechanical, and quantum mechanical/molecular mechanical simulations. , 2007, The Journal of chemical physics.

[25]  Ken A Dill,et al.  Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations. , 2007, Journal of chemical theory and computation.

[26]  B. Trout,et al.  Obtaining reaction coordinates by likelihood maximization. , 2006, The Journal of chemical physics.

[27]  Preston Moore,et al.  Metadynamics as a tool for exploring free energy landscapes of chemical reactions. , 2006, Accounts of chemical research.

[28]  C. Dellago,et al.  Equilibrium free energies from fast-switching trajectories with large time steps. , 2005, The Journal of chemical physics.

[29]  G. Hummer,et al.  Reaction coordinates and rates from transition paths. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[30]  Aaron R Dinner,et al.  Automatic method for identifying reaction coordinates in complex systems. , 2005, The journal of physical chemistry. B.

[31]  Radford M. Neal Taking Bigger Metropolis Steps by Dragging Fast Variables , 2005, math/0502099.

[32]  W. E,et al.  Finite temperature string method for the study of rare events. , 2002, The journal of physical chemistry. B.

[33]  A. Berezhkovskii,et al.  One-dimensional reaction coordinates for diffusive activated rate processes in many dimensions. , 2005, The Journal of chemical physics.

[34]  D. Frenkel Speed-up of Monte Carlo simulations by sampling of rejected states. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[35]  D. Case,et al.  Constant pH molecular dynamics in generalized Born implicit solvent , 2004, J. Comput. Chem..

[36]  Scott Brown,et al.  Cool walking: A new Markov chain Monte Carlo sampling method , 2003, J. Comput. Chem..

[37]  Tim Hesterberg,et al.  Monte Carlo Strategies in Scientific Computing , 2002, Technometrics.

[38]  M. Athènes Computation of a chemical potential using a residence weight algorithm. , 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.

[39]  P. Kollman,et al.  Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation , 2002, Proteins.

[40]  David Chandler,et al.  Transition path sampling: throwing ropes over rough mountain passes, in the dark. , 2002, Annual review of physical chemistry.

[41]  J. Schofield,et al.  Extended state-space Monte Carlo methods. , 2001, Physical review. E, Statistical, nonlinear, and soft matter physics.

[42]  G. Crooks Path-ensemble averages in systems driven far from equilibrium , 1999, cond-mat/9908420.

[43]  C. Jarzynski Hamiltonian Derivation of a Detailed Fluctuation Theorem , 1999, cond-mat/9908286.

[44]  G. Crooks Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences. , 1999, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[45]  Paul Gustafson,et al.  A guided walk Metropolis algorithm , 1998, Stat. Comput..

[46]  David M. Ferguson,et al.  Constant temperature simulations using the Langevin equation with velocity Verlet integration , 1998 .

[47]  G. Crooks Nonequilibrium Measurements of Free Energy Differences for Microscopically Reversible Markovian Systems , 1998 .

[48]  C. Jarzynski Nonequilibrium Equality for Free Energy Differences , 1996, cond-mat/9610209.

[49]  B. Leimkuhler,et al.  Symplectic Numerical Integrators in Constrained Hamiltonian Systems , 1994 .

[50]  G. Parisi,et al.  Simulated tempering: a new Monte Carlo scheme , 1992, hep-lat/9205018.

[51]  A. Lyubartsev,et al.  New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles , 1992 .

[52]  Wolff,et al.  Collective Monte Carlo updating for spin systems. , 1989, Physical review letters.

[53]  B. Brooks,et al.  An analysis of the accuracy of Langevin and molecular dynamics algorithms , 1988 .

[54]  A. Kennedy,et al.  Hybrid Monte Carlo , 1988 .

[55]  Wang,et al.  Nonuniversal critical dynamics in Monte Carlo simulations. , 1987, Physical review letters.

[56]  M. Karplus,et al.  Stochastic boundary conditions for molecular dynamics simulations of ST2 water , 1984 .

[57]  H. C. Andersen Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations , 1983 .

[58]  Peter Salamon,et al.  Thermodynamic length and dissipated availability , 1983 .

[59]  W. C. Swope,et al.  A computer simulation method for the calculation of equilibrium constants for the formation of physi , 1981 .

[60]  D. Ermak A computer simulation of charged particles in solution. I. Technique and equilibrium properties , 1975 .

[61]  D. Ermak,et al.  Equilibrium electrostatic effects on the behavior of polyions in solution: polyion-mobile ion interaction , 1974 .

[62]  H. C. Andersen,et al.  Role of Repulsive Forces in Determining the Equilibrium Structure of Simple Liquids , 1971 .

[63]  W. K. Hastings,et al.  Monte Carlo Sampling Methods Using Markov Chains and Their Applications , 1970 .

[64]  Aneesur Rahman,et al.  Correlations in the Motion of Atoms in Liquid Argon , 1964 .

[65]  N. Metropolis,et al.  Equation of State Calculations by Fast Computing Machines , 1953, Resonance.