Well-tempered metadynamics: A smoothly converging and tunable free-energy method

Physical Review Letters

Volumn 100, Issue 2, 2008, Pages

  Barducci, Alessandro ^a,b,c   Bussi, Giovanni ^c   Parrinello, Michele ^c  

^a MUSEO STORICO DELLA FISICA E CENTRO STUDI E RICERCHE ENRICO FERMI   (Italy)

^b INFN SEZIONE DI ROMA   (Italy)

^c ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; COMPUTER SIMULATION; MOLECULAR DYNAMICS; PEPTIDES;

ADAPTIVE BIAS; METADYNAMICS;

FREE ENERGY;

EID: 38349091489     PISSN: 00319007     EISSN: 10797114     Source Type: Journal    
DOI: 10.1103/PhysRevLett.100.020603     Document Type: Article

References (38)

1. C.W. Gear, I.G. Kevrekidis, and C. Theodoropoulos, Comput. Chem. Eng. 26, 941 (2002). CCENDW 0098-1354 10.1016/S0098-1354(02)00020-0
2. G. Hummer and I.G. Kevrekidis, J. Chem. Phys. 118, 10762 (2003). JCPSA6 0021-9606 10.1063/1.1574777
3. G.M. Torrie and J.P. Valleau, J. Comput. Phys. 23, 187 (1977). JCTPAH 0021-9991 10.1016/0021-9991(77)90121-8
4. F. Wang and D.P. Landau, Phys. Rev. Lett. 86, 2050 (2001). PRLTAO 0031-9007 10.1103/PhysRevLett.86.2050
5. E. Darve and A. Pohorille, J. Chem. Phys. 115, 9169 (2001). JCPSA6 0021-9606 10.1063/1.1410978
6. A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 99, 12562 (2002). 10.1073/pnas.202427399
7. S. Marsili, A. Barducci, R. Chelli, P. Procacci, and V. Schettino, J. Phys. Chem. B 110, 14011 (2006). JPCBFK 1520-6106 10.1021/jp062755j
8. C. Micheletti, A. Laio, and M. Parrinello, Phys. Rev. Lett. 92, 170601 (2004). PRLTAO 0031-9007 10.1103/PhysRevLett.92.170601
9. F.L. Gervasio, A. Laio, and M. Parrinello, J. Am. Chem. Soc. 127, 2600 (2005). JACSAT 0002-7863 10.1021/ja0445950
10. B. Ensing and M.L. Klein, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 102, 6755 (2005). 10.1073/pnas.0408094102
11. A.R. Oganov, R. Martonák, A. Laio, P. Raiteri, and M. Parrinello, Nature (London) 438, 1142 (2005). NATUAS 0028-0836 10.1038/nature04439
12. T. Ishikawa, H. Nagara, K. Kusakabe, and N. Suzuki, Phys. Rev. Lett. 96, 095502 (2006). PRLTAO 0031-9007 10.1103/PhysRevLett.96.095502
13. N.N. Nair, E. Schreiner, and D. Marx, J. Am. Chem. Soc. 128, 13815 (2006). JACSAT 0002-7863 10.1021/ja063295a
14. M. Boero, T. Ikeda, E. Ito, and K. Terakura, J. Am. Chem. Soc. 128, 16798 (2006). JACSAT 0002-7863 10.1021/ja064117k
15. G. Bussi, F.L. Gervasio, A. Laio, and M. Parrinello, J. Am. Chem. Soc. 128, 13435 (2006). JACSAT 0002-7863 10.1021/ja062463w
16. P.P. Kumar, A.G. Kalinichev, and R.J. Kirkpatrick, J. Chem. Phys. 126, 204315 (2007). JCPSA6 0021-9606 10.1063/1.2741552
17. V. Spiwok, P. Lipovová, and B. Králová, J. Phys. Chem. B 111, 3073 (2007). JPCBFK 1520-6106 10.1021/jp068587c
18. J.-G. Lee, E. Asciutto, V. Babin, C. Sagui, T. Darden, and C. Roland, J. Phys. Chem. B 110, 2325 (2006). JPCBFK 1520-6106 10.1021/jp055809i
19. T. Huber, A.E. Torda, and W.F. van Gunsteren, J. Comput.-Aided Mol. Des. 8, 695 (1994). JCADEQ 0920-654X 10.1007/BF00124016
20. G. Bussi, A. Laio, and M. Parrinello, Phys. Rev. Lett. 96, 090601 (2006). PRLTAO 0031-9007 10.1103/PhysRevLett.96.090601
21. A. Laio, A. Rodriguez-Fortea, F.L. Gervasio, M. Ceccarelli, and M. Parrinello, J. Phys. Chem. B 109, 6714 (2005). JPCBFK 1520-6106 10.1021/jp045424k
22. Y. Wu, J.D. Schmitt, and R. Car, J. Chem. Phys. 121, 1193 (2004). JCPSA6 0021-9606 10.1063/1.1765651
23. V. Babin, C. Roland, T.A. Darden, and C. Sagui, J. Chem. Phys. 125, 204909 (2006). JCPSA6 0021-9606 10.1063/1.2393236
24. D. Min, Y. Liu, I. Carbone, and W. Yang, J. Chem. Phys. 126, 194101 (2007). JCPSA6 0021-9606 10.1063/1.2733648
25. P. Poulain, F. Calvo, R. Antoine, M. Broyer, and P. Dugourd, Phys. Rev. E 73, 056704 (2006). PLEEE8 1063-651X 10.1103/PhysRevE.73.056704
26. A. Harju, B. Barbiellini, S. Siljamäki, R.M. Nieminen, and G. Ortiz, Phys. Rev. Lett. 79, 1173 (1997). PRLTAO 0031-9007 10.1103/PhysRevLett.79.1173
27. J.C. Spall, Introduction to Stochastic Search and Optimization (Wiley, Hoboken, New Jersey, 2003).
28. R.E. Belardinelli and V.D. Pereyra, Phys. Rev. E 75, 046701 (2007). PLEEE8 1063-651X 10.1103/PhysRevE.75.046701
29. J. VandeVondele and U. Rothlisberger, J. Phys. Chem. B 106, 203 (2002). JPCBFK 1520-6106 10.1021/jp013346k
30. L. Rosso, P. Mináry, Z. Zhu, and M.E. Tuckerman, J. Chem. Phys. 116, 4389 (2002). JCPSA6 0021-9606 10.1063/1.1448491
31. L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006). CHPLBC 0009-2614 10.1016/j.cplett.2006.05.062
32. L. Maragliano, A. Fischer, E. Vanden-Eijnden, and G. Ciccotti, J. Chem. Phys. 125, 024106 (2006). JCPSA6 0021-9606 10.1063/1.2212942
33. D. Branduardi, F.L. Gervasio, and M. Parrinello, J. Chem. Phys. 126, 054103 (2007). JCPSA6 0021-9606 10.1063/1.2432340
34. J.A.D. MacKerell, D. Bashford, M. Bellott, R.L. Dunbrack, Jr., J.D. Evanseck, M.J. Field, S. Fischer, J. Gao, H. Guo, and S. Ha, J. Phys. Chem. B 102, 3586 (1998). JPCBFK 1520-6106 10.1021/jp973084f
35. P. Procacci, T.A. Darden, E. Paci, and M. Marchi, J. Comput. Chem. JCCHDD 0192-8651 18, 1848 (1997). 10.1002/(SICI)1096-987X(19971130)18:15<1848:: AID-JCC2>3.0.CO;2-O
36. G. Bussi, D. Donadio, and M. Parrinello, J. Chem. Phys. 126, 014101 (2007). JCPSA6 0021-9606 10.1063/1.2408420
37. P. Raiteri, A. Laio, F.L. Gervasio, C. Micheletti, and M. Parrinello, J. Phys. Chem. B 110, 3533 (2006). JPCBFK 1520-6106 10.1021/jp054359r
38. S. Piana and A. Laio, J. Phys. Chem. B 111, 4553 (2007). JPCBFK 1520-6106 10.1021/jp067873l