A simplified confinement method for calculating absolute free energies and free energy and entropy differences

Journal of Physical Chemistry B

Volumn 117, Issue 3, 2013, Pages 750-762

  Ovchinnikov, Victor ^a   Cecchini, Marco ^b   Karplus, Martin ^a,b  

^a HARVARD UNIVERSITY   (United States)

^b UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; ELECTRON ENERGY LEVELS; ENTHALPY; ENTROPY; INTEGRATION; MOLECULAR DYNAMICS;

ALANINE DIPEPTIDES; BIOMOLECULAR SYSTEM; CODE MODIFICATIONS; CONFIGURATIONAL ENTROPY; CONVERGENCE CRITERION; CONVERGENCE PROPERTIES; DIAGONALIZATIONS; DIATOMIC MOLECULES; ENERGY VALUE; ENTHALPY DIFFERENCES; EXACT RESULTS; FREE-ENERGY DIFFERENCE; IMPLICIT SOLVENTS; IN-VACUUM; MACROSTATES; MOLECULAR FORCE FIELD; NORMAL MODES; ROBUST FORMULATIONS; SIMULATION TIME; THERMODYNAMIC INTEGRATION;

FREE ENERGY;

EID: 84872850584     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp3080578     Document Type: Article

References (75)

1. Kollmann, P. Chem. Rev. 1993, 93, 2395-2417
2. Frenkel, D.; Smit, B. Understanding Molecular Simulation: From Algorithms to Applications, 2 nd ed.; Academic Press: San Diego, CA, 2001.
3. Torrie, G.; Valleau, J. J. Comput. Phys. 1977, 23, 187-199
4. Czerminski, R.; Elber, R. J. Chem. Phys. 1990, 92, 5580-5601
5. Bartels, C.; Schaefer, M.; Karplus, M. J. Chem. Phys. 1999, 111, 8048
6. Laio, A.; Parrinello, M. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 12562
7. Hénin, J.; Chipot, C. J. Chem. Phys. 2005, 123, 244906
8. Maragliano, L.; Fischer, A.; Vanden-Eijnden, E.; Ciccotti, G. J. Chem. Phys. 2006, 125, 024106
9. Branduardi, D.; Gervasio, F.; Parrinello, M. J. Chem. Phys. 2007, 126, 054103
10. Ovchinnikov, V.; Cecchini, M.; Vanden-Eijnden, E.; Karplus, M. Biophys. J. 2011, 101, 2436-2444
11. Stoessel, J.; Nowak, P. Macromolecules 1990, 23, 1961-1965
12. Tyka, M.; Clarke, A.; Sessions, R. J. Phys. Chem. B 2006, 110, 17212-17220
13. Cecchini, M.; Krivov, S.; Spichty, M.; Karplus, M. J. Phys. Chem. B 2009, 113, 9728-9740
14. Hill, T. L. An Introduction To Statistical Thermodynamics; Dover: New York, 1986.
15. Hoover, W.; Gray, S.; Johnson, K. J. Chem. Phys. 1971, 51, 1128
16. Frenkel, D.; Ladd, D. J. Chem. Phys. 1984, 81, 3188
17. de Koning, M.; Antonelli, A. Phys. Rev. E 1996, 53, 465-474
18. Karplus, M.; Kushick, J. Macromolecules 1981, 14, 325-332
19. Levy, R. M.; Karplus, M.; Kushick, J.; Perahia, D. Macromolecules 1984, 17, 1370-1374
20. Karplus, M.; Ichiye, T.; Pettitt, B. Biophys. J. 1987, 52, 1083-1085
21. Ytreberg, F.; Zuckerman, D. J. Chem. Phys. 2006, 124, 104105
22. Hensen, U.; Grubmüller, H.; Lange, O. PLoS One 2010, 5, e9179
23. Park, S.; Lau, A. Y.; Roux, B. J. Chem. Phys. 2008, 129, 134102
24. Shalloway, D. J. Chem. Phys. 1996, 105, 9986-10007
25. Cheluvaraja, S.; Meirovitch, H. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 9241-9246
26. Grubmüller, H. Phys. Rev. E 1995, 52, 2893-2906
27. Laplace, P. Stat. Sci. 1986, 1, 364-378
28. Kirkwood, J. J. Chem. Phys. 1935, 3, 300-313
29. Kabsch, W. Acta Crystallogr. 1976, A32, 922-923
30. Coutsias, E.; Seok, C.; Dill, K. J. Comput. Chem. 2004, 25, 1849-1857
31. Ovchinnikov, V.; Karplus, M. J. Phys. Chem. B 2012, 116, 8584-8603
32. Brooks, B.; Brooks, C., III; Mackerell, A., Jr.; Nilsson, L.; Petrella, R.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S. J. Comput. Chem. 2009, 30, 1545-1614
33. Phillips, J.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R.; Kale, L.; Schulten, K. J. Comput. Chem. 2005, 26, 1781-1802
34. Bonomi, M.; Branduardi, D.; Bussi, G.; Camilloni, C.; Provasi, D.; Raiteri, P.; Donadio, D.; Marinelli, F.; Pietrucci, F.; Broglia, R. A. Comput. Phys. Commun. 2009, 180, 1961-1972
35. Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. Comput. Phys. 1977, 23, 327-341
36. Wan, S.; Stote, R.; Karplus, M. J. Chem. Phys. 2004, 121, 9539
37. Meirovitch, H.; Cheluvaraja, S.; White, R. P. Curr. Protein Pept. Sci. 2009, 10, 229-243
38. Ward, J. M.; Gorenstein, N. M.; Tian, J.; Martin, S. F.; Post, C. B. J. Am. Chem. Soc. 2010, 132, 11058-11070
39. Jarzynski, C. Phys. Rev. Lett. 1997, 78, 2690-2693
40. Park, S.; Khalili-Araghi, F.; Tajkhorshid, E.; Schulten, K. J. Phys. Chem. 2003, 119, 3559-3566
41. Tirion, M. Phys. Rev. Lett. 1996, 77, 1905-1909
42. Lilliefors, H. J. Am. Stat. Assoc. 1967, 62, 399-402
43. Marcinkiewics, J. In Collected Papers; Zygmund, A., Ed.; Pan′stwowe Wydawnictwo Naukowe: Warsaw, 1964; pp 463-469.
44. Elkin, M.; Andre, I.; Lukatsky, D. J. Stat. Phys. 2012, 1-8
45. Tyka, M.; Clarke, A.; Sessions, R. J. Phys. Chem. B 2007, 111, 9571-9580
46. Neria, E.; Fischer, S.; Karplus, M. J. Chem. Phys. 1996, 105, 1902-1921
47. Brünger, A.; Brooks, C.; Karplus, M. Chem. Phys. Lett. 1984, 105, 495-499
48. Hermans, J. Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 3095-3096
49. Blondel, A.; Karplus, M. J. Comput. Chem. 1996, 17, 1132-1141
50. Brooks, B.; Janežič, D.; Karplus, M. J. Comput. Chem. 1995, 16, 1522-1542
51. Shannon, C. Bell Labs Tech. J. 1948, 27, 379-423
52. 623-656.
53. Reif, F. Fundamentals of Statistical and Thermal Physics, 1 st ed.; McGraw-Hill: New York, 1965.
54. Muñoz, V.; Thompson, P. A.; Hofrichter, J.; Eaton, W. Nature 1997, 390, 196-199
55. Dinner, A.; Lazaridis, T.; Karplus, M. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 9068-9073
56. Pande, V. S.; Rokhsar, D. S. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 9062-9067
57. Klimov, D.; Thirumalai, D. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 2544-2549
58. Gronenborn, A.; Filpula, D.; Essig, N.; Achari, A.; Whitlow, M.; Wingfield, P.; Clore, G. Science 1991, 253, 657-661
59. Bussi, G.; Gervasio, F. L.; Laio, A.; Parrinello, M. J. Am. Chem. Soc. 2006, 128, 13435-13441
60. Spichty, M.; Cecchini, M.; Karplus, M. J. Phys. Chem. Lett. 2010, 1, 1922-1926
61. Zhou, R. Proteins: Struct., Funct., Genet. 2003, 53, 148-161
62. Blanco, F.; Rivas, G.; Serrano, L. Nat. Struct. Biol. 1994, 1, 584
63. MacKerell, A., Jr.; Feig, M.; Brooks, C., III. J. Comput. Chem. 2004, 25, 1400-1415
64. Best, R.; Zhu, X.; Shim, J.; Lopes, P.; Mittal, J.; Feig, M.; MacKerell, A., Jr. J. Chem. Theory Comput. 2012, 8, 3257-3273
65. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179-5197
66. Best, R.; Buchete, N.-V.; Hummer, G. Biophys. J. 2008, 95, L07-L09
67. Piana, S.; Lindorff-Larsen, K.; Shaw, D. Biophys. J. 2011, 100, L47-L49
68. Brooks, B.; Bruccoleri, R.; Olafson, B.; States, D.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217
69. Haberthür, U.; Caflisch, A. J. Comput. Chem. 2007, 29, 701-715
70. MATLAB, version 7.10.0 (R2010a); The MathWorks Inc.: Natick, MA, 2010.
71. Privalov, P. Adv. Protein Chem. 1979, 33, 167
72. Brooks, B.; Karplus, M. Proc. Natl. Acad. Sci. U.S.A. 1983, 80, 6571-6575
73. Tidor, B.; Karplus, M. J. Mol. Biol. 1994, 238, 405-414
74. Wang, J.; Deng, Y.; Roux, B. Biophys. J. 2006, 91, 2798-2814
75. Boresch, S.; Karplus, M. J. Chem. Phys. 1996, 105, 5145-5154