Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation (Proceedings of the National Academy of Sciences of the United States of America (2011) 108, 45 (E1009-E1018) 10.1073/pnas.1106094108);Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue 45, 2011, Pages 9665-

  Nilmeier, Jerome P ^a   Crooks, Gavin E ^b   Minh, David D L ^c   Chodera, John D ^d  

^a LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c ARGONNE NATIONAL LABORATORY   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Expanded ensembles; Markov chain Monte Carlo; Metropolis Hastings; Molecular dynamics

Indexed keywords

DIMER;

ARTICLE; CONTROLLED STUDY; KERNEL METHOD; MONTE CARLO METHOD; NONEQUILIBRIUM CANDIDATE MONTE CARLO METHOD; PRIORITY JOURNAL; PROBABILITY; THERMODYNAMICS; VACUUM;

EID: 81055141412     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1207617109     Document Type: Erratum

References (66)

1. Liu JS (2002) Monte Carlo Strategies in Scientific Computing (Springer, New York), 2nd Ed.
2. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (1953) Equation of state calculations by fast computing machines. J Chem Phys 21:1087-1092.
3. Hastings WK (1970) Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57:97-109.
4. Rahman A (1964) Correlations in the motion of atoms in liquid argon. Phys Rev 136:A405-A411.
5. Swendsen RH, Wang J-S (1987) Nonuniversal critical dynamics in Monte Carlo simulations. Phys Rev Lett 58:86-88.
6. Wolff U (1989) Collective Monte Carlo updating for spin systems. Phys Rev Lett 62:361-364.
7. Neal RM (2004) Taking bigger Metropolis steps by dragging fast variables. (Department of Statistics, University of Toronto, Toronto), Technical Report 0411.
8. Andrieu C, Doucet A, Holenstein R (2010) Particle Markov chain Monte Carlo methods. J R Stat Soc Series B Stat Methodol 72:269-342.
9. Athènes M (2002) Computation of a chemical potential using a residence weight algorithm. Phys Rev E 66:046705.
10. Bürgi R, Kollman PA, van Gunsteren WF (2002) Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation. Proteins 47:469-480. (Pubitemid 34614726)
11. Stern HA (2007) Molecular simulation with variable protonation states at constant pH. J Chem Phys 126:164112.
12. Nilmeier J, Jacobson MP (2009) Monte Carlo sampling with hierarchical move sets: POSH Monte Carlo. J Chem Theor Comput 1968-1984.
13. Opps SB, Schofield J (2001) Extended state-space Monte Carlo methods. Phys Rev E 63:56701.
14. Brown S, Head-Gordon T (2003) Cool walking: A new Markov chain Monte Carlo sampling method. J Comput Chem 24:68-76.
15. Ballard AJ, Jarzynski C (2009) Replica exchange with nonequilibrium switches. Proc Natl Acad Sci USA 106:12224-12229.
16. Lyubartsev AP, Martsinovski AA, Shevkunov SV, Vorontsov-Velyaminov PN (1992) New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles. J Chem Phys 96:1776-1783.
17. Park S (2008) Comparison of the serial and parallel algorithms of generalized ensemble simulations: An analytical approach. Phys Rev E 77:016709.
18. Shirts MR, Chodera JD (2008) Statistically optimal analysis of samples from multiple equilibrium states. J Chem Phys 129:124105.
19. Marinari E, Parisi G (1992) Simulated tempering: A new Monte Carlo scheme. Europhys Lett 19:451-458.
20. Li H, Fajer M, Yang W (2007) 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. J Chem Phys 126:024106.
21. Mongan J, Case DA, McCammon JA (2004) Constant pH molecular dynamics in generalized Born implicit solvent. J Comput Chem 25:2038-2048.
22. Jarzynski C (2000) Hamiltonian derivation of a detailed fluctuation theorem. J Stat Phys 98:77-102.
23. Swope WC, Andersen HC, Berens PH, Wilson KR (1982) A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: Application to small water clusters. J Chem Phys 76:637-649.
24. Ermak DL, Yeh Y (1974) Equilibrium electrostatic effects on the behavior of polyions in solution: Polyion-mobile ion interaction. Chem Phys Lett 24:243-248.
25. Ermak DL (1975) A computer simulation of charged particles in solution. I. Technique and equilibrium properties. J Chem Phys 62:4189-4196.
26. Frenkel D (2004) Speed-up of Monte Carlo simulations by sampling of rejected states. Proc Natl Acad Sci USA 101:17571-17575.
27. Duane S, Kennedy AD, Pendleton BJ, Roweth D (1987) Hybrid Monte Carlo. Phys Lett B 195:216-222.
28. Lelièvre T, Stoltz G, Rousset M (2010) Langevin dynamics with constraints and computation of free energy differences. (Imperial College Press, London).
29. Crooks GE (1998) Nonequilibrium measurements of free energy differences for microscopically reversible markovian systems. J Stat Phys 90:1481-1487.
30. Jarzynski C (1997) Nonequilibrium equality for free energy differences. Phys Rev Lett 78:2690-2693.
31. Lechner W, Oberhofer H, Dellago C, Geissler PL (2006) Equilibrium free energies from fast-switching trajectories with large time steps. J Chem Phys 124:044113.
32. Andersen HC (1983) Rattle: A "velocity" version of the Shake algorithm for molecular dynamics calculations. J Comput Phys 52:24-34.
33. Leimkuhler B, Skeel RD (1994) Symplectic numerical integrators in constrained Hamiltonian systems. J Comput Phys 112:117-125. (Pubitemid 124013417)
34. Paterlini MG, Ferguson DM (1998) Constant temperature simulations using the Langevin equation with velocity Verlet integration. Chem Phys 236:243-252.
35. Izaguirre JA, Sweet CR, Pande VS (2010) Multiscale dynamics of macromolecules using normal mode Langevin. Pac Symp Biocomput 15:240-251.
36. Lelièvre T, Stoltz G, Rousset M (2010) Free Energy Computations: A Mathematical Perspective (Imperial College Press, London), 1st Ed.
37. Gustafson P (1998) A guided walk Metropolis algorithm. Stat Comput 8:357-364.
38. Brünger A, Brooks CL, III, Karplus M (1984) Stochastic boundary conditions for molecular dynamics simulations of ST2 water. Chem Phys Lett 105:495-500.
39. Pastor RW, Brooks Br, Szabo A (1988) An analysis of the accuracy of Langevin and molecular dynamics algorithms. Mol Phys 65:1409-1419.
40. Schlick T (2002) Molecular Modeling and Simulation: An Interdisciplinary Guide (Springer, New York), 1st Ed.
41. Weeks JD, Chandler D, Andersen HC (1971) Role of repulsive forces in determining the equilibrium structure of simple liquids. J Chem Phys 54:5237-5247.
42. Chodera JD, Swope WC, Pitera JW, Seok C, Dill KA (2007) Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations. J Chem Theor Comput 3:26-41.
43. Bolhuis PG, Chandler D, Dellago C, Geissler PL (2002) Transition path sampling: Throwing ropes over rough mountain passes, in the dark. Annu Rev Phys Chem 53:291-318.
44. Best RB, Hummer G (2005) Reaction coordinates and rates from transition paths. Proc Natl Acad Sci USA 102:6732-6737. (Pubitemid 40675384)
45. Ma A, Dinner AR (2005) Automatic method for identifying reaction coordinates in complex systems. J Phys Chem B 109:6769-6779. (Pubitemid 40552537)
46. E W, Ren W, Vanden-Eijnden E (2005) Finite temperature string method for the study of rare events. J Phys Chem B 109:6688-6693.
47. Berezhkovskii A, Szabo A (2005) One-dimensional reaction coordinates for diffusive activated rate processes in many dimensions. J Chem Phys 122:014503.
48. Peters B, Trout BL (2006) Obtaining reaction coordinates by likelihood maximization. J Chem Phys 125:054108.
49. Ensing B, de Vivo M, Liu Z, Moore P, Klein ML (2006) Metadynamics as a tool for exploring free energy landscapes of chemical reactions. Acc Chem Res 39:73-81.
50. Schmiedl T, Seifert U (2007) Optimal finite-time processes in stochastic thermodynamics. Phys Rev Lett 98:108301.
51. Then H, Engel A (2008) Computing the optimal protocol for finite-time processes in stochastic thermodynamics. Phys Rev E 77:041105.
52. Gomez-Marin A, Schmiedl T, Seifert U (2008) Optimal protocols for minimal work processes in underdamped statistical thermodynamics. J Chem Phys 129:024114.
53. Salamon P, Berry RS (1983) Thermodynamic length and dissipated availability. Phys Rev Lett 51:1127-1130.
54. Crooks GE (2007) Measuring thermodynamic length. Phys Rev Lett 99:100602.
55. Feng EH, Crooks GE (2009) Far-from-equilibrium measurements of thermodynamic length. Phys Rev E 79:012104.
56. Minh DDL, Chodera JD (2011) Multiple-timeslice nonequilibrium estimators: Estimating equilibrium ensemble averages from nonequilibrium experiments using multiple timeslices, with application to thermodynamic length. J Chem Phys 134:024111.
57. Shenfeld DK, Xu H, Eastwood MP, Dror RO, Shaw DE (2009) Minimizing thermodynamic length to select intermediate states for free-energy calculations and replicaexchange simulations. Phys Rev E 80:046705.
58. Minh DDL, Adib AB (2008) Optimized free energies from bidirectional single-molecule force spectroscopy. Phys Rev Lett 100:180602.
59. Minh DDL, Chodera JD (2009) Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages. J Chem Phys 131:134110.
60. Crooks GE (1999) Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences. Phys Rev E 60:2721-2726.
61. Crooks GE (2000) Path-ensemble averages in systems driven far from equilibrium. Phys Rev E 61:2361-2366.
62. Athènes M, Marinica M-C (2010) Free energy reconstruction from steered dynamics without post-processing. J Chem Phys 229:7129-7146.
63. Friedrichs MS, et al. (2009) Accelerating molecular dynamic simulation on graphics processing units. J Comput Chem 30:864-872.
64. Eastman P, Pande VS (2010) OpenMM: A hardware-independent framework for molecular simulations. Comput Sci Eng 12:34-39.
65. Eastman P, Pande VS (2010) Efficient nonbonded interactions for molecular dynamics of a graphics processing unit. J Comput Chem 31:1268-1272.
66. Bruns CM, Radmer RA, Chodera JD, Pande VS (2010) PyOpenMM. http://simtk.org/ home/pyopenmm.