How hot? Systematic convergence of the replica exchange method using multiple reservoirs

Journal of Computational Chemistry

Volumn 31, Issue 3, 2010, Pages 620-627

  Ruscio, Jory Z ^a   Fawzi, Nicolas L ^b   Head Gordon, Teresa ^a,b  

^a University of California at Berkeley   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Bimolecular simulation; Enhanced sampling; NMR; Replica exchange

Indexed keywords

ENHANCED SAMPLING; EQUILIBRIUM CONFORMATION; EXPLICIT WATER; FASTER CONVERGENCE; FINITE NUMBER; HIGH TEMPERATURE; HIGHER TEMPERATURES; HIGHEST TEMPERATURE; INTERMEDIATE TEMPERATURES; MULTIPLE PROCESSORS; OPTIMAL TEMPERATURE; OVERALL EFFECTIVENESS; OVERHAUSER EFFECT; REPLICA EXCHANGE; REPLICA EXCHANGE METHOD; REPLICA-EXCHANGE MOLECULAR DYNAMICS SIMULATIONS; SUBREPLICAS; TARGET TEMPERATURE; TEMPERATURE RANGE; THERMO DYNAMIC ANALYSIS;

COMPUTATIONAL EFFICIENCY; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; RESERVOIRS (WATER); THERMOANALYSIS;

TEMPERATURE;

AMYLOID BETA PROTEIN; AMYLOID BETA PROTEIN (21 30); AMYLOID BETA-PROTEIN (21-30); PEPTIDE FRAGMENT; WATER;

ARTICLE; CHEMISTRY; ENERGY TRANSFER; MOLECULAR DYNAMICS; SPECTROSCOPY; TEMPERATURE;

AMYLOID BETA-PROTEIN; ENERGY TRANSFER; MOLECULAR DYNAMICS SIMULATION; PEPTIDE FRAGMENTS; SPECTRUM ANALYSIS; TEMPERATURE; WATER;

EID: 75649134635     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21355     Document Type: Article

References (33)

1. Hukushima, K.; Nemoto, K. J Phys Soc Jpn 1996, 65, 1604.
2. Hansmann, U. H. E. Chem Phys Lett 1997, 281, 140.
3. Sugita, Y.; Okamoto, Y. Chem Phys Lett 1999, 314, 141.
4. Wang, J.-S.; Swendsen, R. H. Phys Rev B: Condens Matter 1988, 37, 7745.
5. Marinari, E.; Parisi, G. Europhys Lett 1992, 19, 451.
6. Rathore, N.; Chopra, M.; de Pablo, J. J Chem Phys 2005, 122, 024111.
7. Nadler, W.; Hansmann, U. H. E. Phys Rev E: Stat Phys Plasmas Fluids Relat Interdiscip Top 2007, 76, 065701.
8. Nymeyer, H. J Chem Theory Comput 2008, 4, 626.
9. Zheng, W. H.; Andrec, M.; Gallicchio, E.; Levy, R. M. Proc Natl Acad Sci USA 2007, 104, 15340.
10. Fukunishi, H.; Watanabe, O.; Takada, S. J Chem Phys 2002, 116,9058.
11. Rick, S. W. J Chem Phys 2007, 126, 054102.
12. Sindhikara, D.; Meng, Y. L.; Roitberg, A. E. J Chem Phys 2008, 128, 024103.
13. Hagen, M.; Kim, B.; Liu, P.; Friesner, R. A.; Berne, B. J Phys Chem B 2007, 111, 1416.
14. Gallicchio, E.; Levy, R. M.; Parashar, M. J Comput Chem 2008, 29, 788.
15. Andricioaei, I.; Straub, J. E.; Voter, A. F. J Chem Phys 2001, 114,6994.
16. Brown, S.; Head-Gordon, T. J Comput Chem 2003, 24, 68.
17. Frantz, D. D.; Freeman, D. L.; Doll, J. D. J Chem Phys 1990,93, 2769.
18. Zhou, R.; Berne, B. J. J Chem Phys 1997, 107, 9185.
19. Liu, P.; Kim, B.; Friesner, R. A.; Berne, B. J. Proc Natl Acad Sci USA 2005, 102, 13749.
20. Okur, A.; Wickstrom, L.; Layten, M.; Geney, R.; Song, K.; Hornak, V.; Simmerling, C. J Chem Theory Comput 2006, 2, 420.
21. Periole, X.; Mark, A. E. J Chem Phys 2007, 126, 014903.
22. Zuckerman, D. M.; Lyman, E. J Chem Theory Comput 2006, 2, 12001202.
23. Opps, S. B.; Schofield, J. Phys Rev E: Stat Phys Plasmas Fluids Relat Interdiscip Top 2001, 63, 056701.
24. Okur, A.; Roe, D. R.; Cui, G.; Hornak, V.; Simmerling, C. J Chem Theory Comput 2007, 3, 557.
25. Roitberg, A. E.; Okur, A.; Simmerling, C. J Phys Chem B 2007, 111, 2415.
26. Huang, X.; Bowman, G. R.; Pande, V. S. J Chem Phys 2008, 128, 205106.
27. Thirumalai, D.; Mountain, R. D.; Kirkpatrick, T. R. Phys Rev A: At Mol Opt Phys 1989, 39, 3563.
28. Case, D.A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Crowley, M.; Walker, R. C.; Zhang, W.; Merz, K. M.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Kolossváry, I.; Wong, K. F.; Paesani, F.; Vanicek, J.; Wu, X.; Brozell, S. R.; Steinbrecher, T.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Mathews, D. H.; Seetin, M. G.; Sagui, C.; Babin, V.; Kollman, P. A. University of California: San Francisco, 2008.
29. Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Proteins 2006, 65, 712.
30. Horn, H. W.; Swope, W. C.; Pitera, J. W.; Madura, J. D.; Dick, T. J.; Hura, G. L.; Head-Gordon, T. J Chem Phys 2004, 120, 9665.
31. Fawzi, N. L.; Phillips, A. H.; Ruscio, J. Z.; Doucleff, M.; Wemmer, D. E.; Head-Gordon, T. J Am Chem Soc 2008, 130, 6145.
32. Darden, T.; York, D.; Pedersen, L. J Chem Phys 1993, 98, 10089.
33. Zheng, W.; Andrec, M.; Gallicchio, E.; Levy, R. M. J Phys Chem B 2008, 112, 6083.