ORAC: A molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level

Journal of Computational Chemistry

Volumn 31, Issue 5, 2010, Pages 1106-1116

  Marsili, Simone ^a,b   Signorini, Giorgio Federico ^a,b   Chelli, Riccardo ^a,c   Marchi, Massimo ^d   Procacci, Piero ^a,b  

^a UNIVERSITY OF FLORENCE   (Italy)

^b Centro Interdipartimentale per Lo Studio Delle Dinamiche Complesse (CSDC)   (Italy)

^c UNIVERSITY OF FLORENCE   (Italy)

^d DIF   (France)

Author keywords

Free energy; Metadynamics; Molecular dynamics; Non equilibrium; Replica exchange method; Solute tempering

Indexed keywords

FREE ENERGY; NETWORK ARCHITECTURE; OPEN SOURCE SOFTWARE; PARALLEL ARCHITECTURES; TEMPERING;

COMPUTATIONAL TECHNOLOGY; GNU GENERAL PUBLIC LICENSE; METADYNAMICS; MOLECULAR DYNAMICS SIMULATIONS; NON EQUILIBRIUM; PARTICLE MESH EWALD METHODS; REPLICA EXCHANGE METHOD; STEERED MOLECULAR DYNAMICS;

MOLECULAR DYNAMICS;

BIOPOLYMER; PROTEIN;

ARTICLE; CHEMISTRY; COMPUTER PROGRAM; MOLECULAR DYNAMICS; THERMODYNAMICS;

BIOPOLYMERS; MOLECULAR DYNAMICS SIMULATION; PROTEINS; SOFTWARE; THERMODYNAMICS;

EID: 77953056324     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21388     Document Type: Article

References (59)

1. Frenkel, D.; Smit, B. Understanding Molecular Simulations; Academic Press: San Diego, 1996.
2. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Oxford University Press: Walton Street, Oxford OX2 6DP, 1989.
3. Procacci, P.; Darden, T.; Paci, E.; Marchi, M. J Comput Chem 1997, 18, 1848.
4. Marchi, M.; Procacci, P. J Chem Phys 1998, 109, 5194.
5. Procacci, P.; Marchi, M.; Martyna, G. J. J Chem Phys 1998, 108, 8799.
6. Tuckerman, M. E.; Berne, B.; Martyna, G. J Chem Phys 1992, 97, 1990.
7. Darden, T.; York, D.; Pedersen, L. J Chem Phys 1993, 98, 10089.
8. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J Chem Phys 1995, 101, 8577.
9. Procacci, P.; Darden. T.; Marchi, M. J Phys Chem 1996, 100, 10464.
10. Duan, Y.; Kollman, P. A. Science, 1998, 282, 740.
11. Swendsen, R. H.; Wang, J. S. Phys Rev Lett 1986, 57, 2607.
12. Geyer, C. G. In Computing Science and Statistics, Proceedings of the 23rd Symposium on the Interface, Keramidis E. M., Ed.; Interface Foundation: Fairfax, 1991, p. 156.
13. Marinari, E.; Parisi, G. Europhys Lett 1992, 19, 451.
14. Hukushima, K.; Nemoto, K. J Phys Soc Jpn 1996, 65, 1604.
15. Torrie, G. M.; Valleau, J. P. Chem Phys Lett 1974, 28, 578.
16. Laio, A.; Parrinello, M. Proc Natl Acad Sci USA 2002, 99, 12562.
17. Wang, F.; Landau, D. P. Phys Rev Lett 2001, 86, 2050.
18. Henin. J.; Chipot, C. J Chem Phys 2004, 121, 2904.
19. Marsili, S.; Barducci, A.; Chelli, R.; Procacci, P.; Schettino, V. J Phys Chem B 2006, 110, 14011.
20. Laio, A.; Rodriguez-Fortea, A.; Gervasio, F. L.; Ceccarelli, M; Parrinello, M. J Phys Chem B 2005, 109, 6714.
21. Jarzynski, C. Phys Rev Lett 1997, 78, 2690.
22. Crooks, G. E. J Stat Phys 1998, 90, 1481.
23. Hummer, G.; Szabo, A. Proc Natl Acad Sci USA 2001, 98, 3658.
24. Shirts, M. R.; Bair, E.; Hooker, G; Pande, V. S. Phys Rev Lett 2003, 91, 140601.
25. Chandler, D. Introduction to Modern Statistical Mechanics; Oxford University Press: New York, 1987.
26. Fukunishi, H.; Watanabe, O.; Takada, S. J Chem Phys 2002, 116, 9058.
27. Liu, P.; Kim., B.; Friesner, R. A.; Berne, B. J Proc Acad Sci 2005, 102, 13749.
28. Mezei, M. J Comput Phys 1987, 68, 237.
29. Paine, G. H.; Scheraga, H. A. Biopolymers 1985, 24, 1391.
30. Huber, T.; Torda, A. E; van Gunsteren, W. F. J Comput.-Aided Mol Des 1994, 8, 695.
31. Watanabe, M.; Reinhardt, W. P. Phys Rev Lett 1990, 65, 3301.
32. Kampen, N. G. V. Stochastic Processes in Physics and Chemistry; North-Holland: Amsterdam, 1992.
33. Iannuzzi, M.; Laio, A.; Parrinello, M. Phys Rev Lett 2003, 90, 238302.
34. Babin, V.; Roland, C.; Darden, T. A; Sagui, C. J Chem Phys 2006, 125, 204909.
35. Lucy, L. B. Astronom J 1977, 82, 1013.
36. Earl, D. J.; Deem, M. W. J Phys Chem B 2005, 109, 6701.
37. Zhou, C.; Bhatt, R. N. Phys Rev E 2005, 72, 0205701.
38. Belardinelli, R. E.; Pereira, V. D. Phys Rev E 2007, 75, 046701.
39. Barducci, A.; Bussi, C.; Parrinello, M. Phys Rev Lett 2008, 100, 020603.
40. Raiteri, P.; Gervasio, F. L.; Micheletti, C; Parrinello, M. J Phys Chem B 2006, 110, 3533.
41. Isralewitz, B.; Gao, M.; Schulten, K. Curr Opin Struct Biol 2001, 11, 224.
42. Evans, D. J.; Cohen, E. G. D.; Morriss, G. P. Phys Rev Lett 1993, 71, 2401.
43. Evans, D. J.; Searls, D. J. Phys Rev E 1994, 50, 1645.
44. Zwanzig, R. W. J Chem Phys 1954, 22, 1420.
45. Collin, D.; Ritort, F.; Jarzynski, C.; Smith, S.; B. Tinoco, I., Jr; Bustamante, C. Nature 2005, 437, 231.
46. Park, S.; Schulten, K. J Chem Phys 2004, 120, 5946.
47. Procacci, P.; Marsili, S.; Barducci, A.; Signorini, G. F.; Chelli, R. J Chem Phys 2006, 125, 164101.
48. Wood, R. H.; Muehlbauer, W. C. F. J Phys Chem 1991, 95, 6670.
49. Minh, D. D.; Adib, A. B. Phys Rev Lett 2008, 100, 180602.
50. Chelli, R.; Marsili, S.; Procacci, P. Phys Rev E 2008, 77, 031104.
51. Chelli, R.; Procacci, P. Phys Chem Chem Phys 2009, 11, 1152.
52. Crooks, G. E. Phys Rev E 2000, 61, 2361.
53. Bennett, C. H. J Comp Phys 1976, 22, 245.
54. Chelli, R. J Chem Phys 2009, 130, 054102.
55. Crooks, G. E. Excursions in Statistical Dynamics, PhD thesis, University of California, Berkeley, 1999.
56. Jarzynski, C. J Stat Phys 2000, 98, 77.
57. Chelli, R.; Marsili, S.; Barducci, A.; Procacci, P. Phys Rev E 2007, 75, 050101.
58. Chelli, R.; Marsili, S.; Barducci, A.; Procacci, P. J Chem Phys 2007, 127, 034110.
59. Williams, S. R.; Searles, D. J.; Evans, D. J. Phys Rev Lett 2008, 100, 250601.