Self-learning adaptive umbrella sampling method for the determination of free energy landscapes in multiple dimensions

Journal of Chemical Theory and Computation

Volumn 9, Issue 4, 2013, Pages 1885-1895

  Wojtas Niziurski, Wojciech ^a   Meng, Yilin ^b   Roux, Benoiît ^b   Bernèche, Simon ^a  

^a UNIVERSITY OF BASEL   (Switzerland)

^b UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84875967647     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct300978b     Document Type: Article

References (45)

1. Konig, G.; Wu, X. W.; Brooks, B. Crossing energy barriers with self-guided Langevin dynamics Eur. Biophys. J. Biophys. 2011, 40, 108-109
2. Wu, X. W.; Brooks, B. R. Self-guided Langevin dynamics simulation method Chem. Phys. Lett. 2003, 381 (3-4) 512-518
3. Hamelberg, D.; Mongan, J.; McCammon, J. A. Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules J. Chem. Phys. 2004, 120 (24) 11919-11929
4. Voter, A. F. Hyperdynamics: Accelerated molecular dynamics of infrequent events Phys. Rev. Lett. 1997, 78 (20) 3908-3911
5. Fajer, M.; Hamelberg, D.; McCammon, J. A. Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration J. Chem. Theory Comput. 2008, 4 (10) 1565-1569
6. Jiang, W.; Roux, B. Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations J. Chem. Theory Comput. 2010, 6 (9) 2559-2565
7. Bartels, C.; Karplus, M. Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations J. Comput. Chem. 1997, 18 (12) 1450-1462
8. Hooft, R. W. W.; Vaneijck, B. P.; Kroon, J. An Adaptive Umbrella Sampling Procedure in Conformational-Analysis Using Molecular-Dynamics and Its Application to Glycol J. Chem. Phys. 1992, 97 (9) 6690-6694
9. Mezei, M. Adaptive Umbrella Sampling-Self-Consistent Determination of the Non-Boltzmann Bias J. Comput. Phys. 1987, 68 (1) 237-248
10. Roux, B. The Calculation of the Potential of Mean Force Using Computer-Simulations Comput. Phys. Commun. 1995, 91 (1-3) 275-282
11. Torrie, G. M.; Valleau, J. P. Monte-Carlo Free-Energy Estimates Using Non-Boltzmann Sampling-Application to Subcritical Lennard-Jones Fluid Chem. Phys. Lett. 1974, 28 (4) 578-581
12. Bartels, C. Analyzing biased Monte Carlo and molecular dynamics simulations Chem. Phys. Lett. 2000, 331 (5-6) 446-454
13. Ferrenberg, A. M.; Swendsen, R. H. Optimized Monte-Carlo Data-Analysis Phys. Rev. Lett. 1989, 63 (12) 1195-1198
14. Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. The Weighted Histogram Analysis Method for Free-Energy Calculations on Biomolecules. 1. The Method J. Comput. Chem. 1992, 13 (8) 1011-1021
15. Zhu, F. Q.; Hummer, G. Convergence and error estimation in free energy calculations using the weighted histogram analysis method J. Comput. Chem. 2012, 33 (4) 453-465
16. Maragliano, L.; Vanden-Eijnden, E. A temperature accelerated method for sampling free energy and determining reaction pathways in rare events simulations Chem. Phys. Lett. 2006, 426 (1-3) 168-175
17. Darve, E.; Pohorille, A. Calculating free energies using average force J. Chem. Phys. 2001, 115 (20) 9169-9183
18. Darve, E.; Rodriguez-Gomez, D.; Pohorille, A. Adaptive biasing force method for scalar and vector free energy calculations. J. Chem. Phys. 2008, 128, (14).
19. Henin, J.; Fiorin, G.; Chipot, C.; Klein, M. L. Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables J. Chem. Theory Comput. 2010, 6 (1) 35-47
20. Bussi, G.; Laio, A.; Parrinello, M. Equilibrium free energies from nonequilibrium metadynamics Phys. Rev. Lett. 2006, 96 (9) 090601
21. Laio, A.; Parrinello, M. Escaping free-energy minima Proc. Natl. Acad. Sci. U. S. A. 2002, 99 (20) 12562-12566
22. Laio, A.; Rodriguez-Fortea, A.; Gervasio, F. L.; Ceccarelli, M.; Parrinello, M. Assessing the accuracy of metadynamics J. Phys. Chem. B 2005, 109 (14) 6714-6721
23. Zheng, L. Q.; Chen, M. G.; Yang, W. Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems Proc. Natl. Acad. Sci. U. S. A. 2008, 105 (51) 20227-20232
24. Zheng, L. Q.; Chen, M. G.; Yang, W. Simultaneous escaping of explicit and hidden free energy barriers: Application of the orthogonal space random walk strategy in generalized ensemble based conformational sampling J. Chem. Phys. 2009, 130 (23) 234105/1-234105/10
25. Maragliano, L.; Vanden-Eijnden, E. Single-sweep methods for free energy calculations J. Chem. Phys. 2008, 128, 18
26. van Duijneveldt, J. S.; Frenkel, D. Computer-Simulation Study of Free-Energy Barriers in Crystal Nucleation J. Chem. Phys. 1992, 96 (6) 4655-4668
27. E, W.; Ren, W. Q.; Vanden-Eijnden, E. String method for the study of rare events Phys. Rev. B 2002, 66 (5) 052301
28. Maragliano, L.; Fischer, A.; Vanden-Eijnden, E.; Ciccotti, G. String method in collective variables: Minimum free energy paths and isocommittor surfaces J. Chem. Phys. 2006, 125, 2
29. Pan, A. C.; Sezer, D.; Roux, B. Finding transition pathways using the string method with swarms of trajectories J. Phys. Chem. B 2008, 112 (11) 3432-3440
30. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of Simple Potential Functions for Simulating Liquid Water J. Chem. Phys. 1983, 79 (2) 926-935
31. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten, K. Scalable molecular dynamics with NAMD J. Comput. Chem. 2005, 26 (16) 1781-1802
32. MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B 1998, 102 (18) 3586-3616
33. Feller, S. E.; Zhang, Y. H.; Pastor, R. W.; Brooks, B. R. Constant-Pressure Molecular-Dynamics Simulation-the Langevin Piston Method J. Chem. Phys. 1995, 103 (11) 4613-4621
34. Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald-an N.Log(N) Method for Ewald Sums in Large Systems J. Chem. Phys. 1993, 98 (12) 10089-10092
35. Zhou, Y. F.; Morais-Cabral, J. H.; Kaufman, A.; MacKinnon, R. Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0 angstrom resolution Nature 2001, 414 (6859) 43-48
36. Brooks, B. R.; Brooks, C. L.; Mackerell, A. D.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. CHARMM: The Biomolecular Simulation Program J. Comput. Chem. 2009, 30 (10) 1545-1614
37. Roux, B.; Bernèche, S. On the potential functions used in molecular dynamics simulations of ion channels Biophys. J. 2002, 82 (3) 1681-1684
38. Hoover, W. G. Canonical Dynamics-Equilibrium Phase-Space Distributions Phys. Rev. A 1985, 31 (3) 1695-1697
39. Sanbonmatsu, K. Y.; Garcia, A. E. Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics Proteins: Struct., Funct., Bioinf. 2002, 46 (2) 225-234
40. Sugita, Y.; Okamoto, Y. Replica-exchange molecular dynamics method for protein folding Chem. Phys. Lett. 1999, 314 (1-2) 141-151
41. Sutto, L.; D'Abramo, M.; Gervasio, F. L. Comparing the Efficiency of Biased and Unbiased Molecular Dynamics in Reconstructing the Free Energy Landscape of Met-Enkephalin J. Chem. Theory Comput. 2010, 6 (12) 3640-3646
42. Doyle, D. A.; Cabral, J. M.; Pfuetzner, R. A.; Kuo, A. L.; Gulbis, J. M.; Cohen, S. L.; Chait, B. T.; MacKinnon, R. The structure of the potassium channel: Molecular basis of K+ conduction and selectivity Science 1998, 280 (5360) 69-77
43. Bernèche, S.; Roux, B. Energetics of ion conduction through the K+ channel Nature 2001, 414 (6859) 73-77
44. Bernèche, S.; Roux, B. A microscopic view of ion conduction through the K+ channel Proc. Natl. Acad. Sci. U. S. A. 2003, 100 (15) 8644-8648
45. Hodgkin, A. L.; Keynes, R. D. The Potassium Permeability of a Giant Nerve Fibre J. Physiol. (Oxford, U. K.) 1955, 128 (1) 61-88