Equipartition and the calculation of temperature in biomolecular simulations

Journal of Chemical Theory and Computation

Volumn 6, Issue 7, 2010, Pages 2045-2058

  Eastwood, Michael P ^a   Stafford, Kate A ^a,b   Lippert, Ross A ^a   Jensen, Morten Ø ^a   Maragakis, Paul ^a   Predescu, Cristian ^a   Dror, Ron O ^a   Shaw, David E ^a,b  

^a D E SHAW RESEARCH   (United States)

^b Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79251622248     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct9002916     Document Type: Article

References (48)

1. Huang, K. Statistical Mechanics; John Wiley & Sons: New York, 1987.
2. Straub, J. E.; Thirumalai, D. Proteins: Struct., Funct., Genet. 1993, 15, 360-373.
3. Tobias, D. J.; Martyna, G. J.; Klein, M. L. J. Phys. Chem. 1993, 97, 12959-12966.
4. Lingenheil, M.; Denschlag, R.; Reichold, R.; Tavan, P. J. Chem. Theory Comput. 2008, 4, 1293-1306.
5. Feller, S. E.; Zhang, Y.; Pastor, R. W.; Brooks, B. R. J. Chem. Phys. 1995, 103, 4613-4621.
6. Harvey, S. C.; Tan, R. K.-Z.; Cheatham, T. E., III. J. Comput. Chem. 1998, 19, 726-740.
7. Mor, A.; Ziv, G.; Levy, Y. J. Comput. Chem. 2008, 29, 1992- 1998.
8. Levitt, M.; Sharon, R. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 7557-7561.
9. Guenot, J.; Kollman, P. A. Protein Sci. 1992, 1, 1185-1205.
10. Arnold, G. E.; Ornstein, R. L. Proteins: Struct., Funct., Genet. 1994, 18, 19-33.
11. Sagui, C.; Darden, T. A. Annu. Rev. Biophys. Biomol. Struct. 1999, 28, 155-179.
12. Swope, W. C.; Andersen, H. C.; Berens, P. H.; Wilson, K. R. J. Chem. Phys. 1982, 76, 637-649.
13. Allen, M. P.; Tildesley, D. J. Computer simulation of liquids; Oxford University Press: New York, 1989.
14. Ruth, R. D. IEEE Trans. Nucl. Sci. 1983, 30, 2669-2671.
15. Hairer, E.; Lubich, C.; Wanner, G. Geometric Numerical Integration. In Structure-Preserving Algorithms for Ordinary Differential Equations; Volume 31 of Springer Series in Computational Mathematics: Springer: Berlin, Germany, 2006.
16. Tolman, R. C. Phys. Rev. 1918, 11, 261-275.
17. Gans, J.; Shalloway, D. Phys. Rev. E: Stat. Phys., Plasmas, Fluids, Relat. Interdiscip. Top. 2000, 61, 4587-4592.
18. Cuendet, M. A.; van Gunsteren, W. F. J. Chem. Phys. 2007, 127, 184102.
19. MacGowan, D.; Heyes, D. M. Mol. Simul. 1988, 1, 277- 297.
20. Tuckerman, M.; Berne, B. J.; Martyna, G. J. J. Chem. Phys. 1992, 97, 1990-2001.
21. Uline, M. J.; Siderus, D. W.; Corti, D. S. J. Chem. Phys. 2008, 128, 124301.
22. Shirts, R. B.; Burt, S. R.; Johnson, A. M. J. Chem. Phys. 2006, 125, 164102.
23. Leimkuhler, B. J.; Skeel, R. D. J. Comput. Phys. 1994, 112, 117-125.
24. Bond, S. D.; Leimkuhler, B. J. Acta Numerica 2007, 16, 1- 65.
25. Engle, R. D.; Skeel, R. D.; Drees, M. J. Comput. Phys. 2005, 206, 432-452.
26. Zhou, J.; Reich, S.; Brooks, B. R. J. Chem. Phys. 2000, 112, 7919-7929.
27. Brooks, B. R. et al. J. Comput. Chem. 2009, 30, 1545-1614.
28. Izaguirre, J. A.; Hampton, S. S. J. Comput. Phys. 2004, 200, 581-604.
29. Hoover, W. G. Phys. Rev. A: At., Mol., Opt. Phys. 1985, 31, 1695-1697.
30. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690.
31. Sugita, Y.; Okamoto, Y. Chem. Phys. Lett. 1999, 314, 141- 151.
32. Bowers, K. J.; Chow, E.; Xu, H.; Dror, R. O.; Eastwood, M. P.; Gregersen, B. A.; Klepeis, J. L.; Kolossváry, I.; Moraes, M. A.; Sacerdoti, F. D.; Salmon, J. K.; Shan, Y.; Shaw, D. E. Novel Algorithms for Scalable Molecular Dynamics Simulations on Commodity Clusters. In Proceedings of the ACM/IEEE Conference on Supercomputing (SC06); ACM/IEEE Conference on Supercomputing (SC06), Tampa, FL, November 11-17, 2006; ACM Press: New York, 2006.
33. Flyvbjerg, H.; Petersen, H. G. J. Chem. Phys. 1989, 91, 461- 466.
34. Kaminski, G.; Friesner, R. A.; Tirado-Rives, J.; Jorgensen, W. L. J. Phys. Chem. B 2001, 105, 6474-6487.
35. Maragakis, P.; Lindorff-Larsen, K.; Eastwood, M. P.; Dror, R. O.; Klepeis, J. L.; Arkin, I. T.; Jensen, M. Ø.; Xu, H.; Trbovic, N.; Friesner, R. A.; Palmer, A. G. III.; Shaw, D. E. J. Phys. Chem. B 2008, 112, 6155-6158.
36. Cornilescu, G.; Marquardt, J. L.; Ottiger, M.; Bax, A. J. Am. Chem. Soc. 1998, 120, 6836-6837.
37. Lindahl, E.; Hess, B.; van der Spoel, D. J. Mol. Mod. 2001, 7, 306-317.
38. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. Interaction models for water in relation to protein hydration. In Intermolecular Forces; Pullman, B., Ed.; D. Reidel Publishing Company: Dordrecht, The Netherlands, 1981.
39. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089-10092.
40. Kräutler, V.; Van Gunsteren, W. F.; Hünenberger, P. H. J. Comput. Chem. 2001, 22, 501-508.
41. Lippert, R. A.; Bowers, K. J.; Dror, R. O.; Eastwood, M. P.; Gregersen, B. A.; Klepeis, J. L.; Kolossváry, I.; Shaw, D. E. J. Chem. Phys. 2007, 126, 046101.
42. Tuckerman, M. E.; Berne, B. J.; Martyna, G. J.; Klein, M. L. J. Chem. Phys. 1993, 99, 2796-2808.
43. Mazur, A. K. J. Comput. Phys. 1997, 136, 354-365.
44. Feenstra, K. A.; Hess, B.; Berendsen, H. J. C. J. Comput. Chem. 1999, 20, 786-798.
45. Shaw, D. E. et al. Anton, a special-purpose machine for molecular dynamics simulation. In Proceedings of the 34th Annual International Symposium on Computer Architecture (ISCA '07); 34th Annual International Symposium on Computer Architecture (ISCA '07), San Diego, CA, June 9-13, 2007ACM Press: New York, 2007.
46. Case, D. A. Curr. Opin. Struct. Biol. 1994, 4, 285-290.
47. Oda, K.; Miyagawa, H.; Kitamura, K. Mol. Simul. 1996, 16, 167-177.
48. Pastor, R. W.; Brooks, B. R.; Szabo, A. Mol. Phys. 1988, 65, 1409-1419.