Calculating position-dependent diffusivity in biased molecular dynamics simulations

Journal of Chemical Theory and Computation

Volumn 9, Issue 2, 2013, Pages 876-882

  Comer, Jeffrey ^a,b   Chipot, Christophe ^c,d   González Nilo, Fernando D ^a,b,e  

^a Centro de Innovación UC Anacleto Angelini   (Chile)

^b UNIVERSIDAD ANDRÉS BELLO   (Chile)

^c UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^d UNIVERSITÉ DE LORRAINE   (France)

^e UNIVERSIDAD DE VALPARAÍSO   (Chile)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84873665160     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct300867e     Document Type: Article

References (39)

1. Kramers, H. Physica 1940, 7, 284-304
2. Zwanzig, R. J. Stat. Phys. 1983, 30, 255-262
3. Hummer, G. New J. Phys. 2005, 7, 34
4. Forney, M.; Janosi, L.; Kosztin, I. Phys. Rev. E 2008, 78, 051913
5. Chipot, C.; Pohorille, A. Free Energy Calculations; Springer: Berlin, 2007.
6. Lelièvre, T.; Stoltz, G.; Rousset, M. Free Energy Computations: A Mathematical Perspective; World Scientific: Singapore, 2010.
7. Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. J. Comput. Chem. 1992, 13, 1011-1021
8. Roux, B. Comput. Phys. Commun. 1995, 91, 275-282
9. Jarzynski, C. Phys. Rev. Lett. 1997, 78, 2690-2693
10. Crooks, G. E. Phys. Rev. E 1999, 60, 2721-6
11. Darve, E.; Rodríguez-Gómez, D.; Pohorille, A. J. Chem. Phys. 2008, 128, 144120
12. Hénin, J.; Fiorin, G.; Chipot, C.; Klein, M. J. Chem. Theory Comput. 2009, 6, 35-47
13. Bussi, G.; Laio, A.; Parrinello, M. Phys. Rev. Lett. 2006, 96, 90601
14. Zwanzig, R. Proc. Natl. Acad. Sci. U. S. A. 1988, 85, 2029
15. Mamonov, A.; Kurnikova, M.; Coalson, R. Biophys. Chem. 2006, 124, 268-278
16. Marrink, S.; Berendsen, H. J. Phys. Chem. 1994, 98, 4155-68
17. Woolf, T.; Roux, B. Proc. Natl. Acad. Sci. U. S. A. 1994, 91, 11631
18. Luo, Y.; Egwolf, B.; Walters, D.; Roux, B. J. Phys. Chem. B 2009, 2035-2042
19. Comer, J.; Aksimentiev, A. J. Phys. Chem. C 2012, 116, 3376-3393
20. Hénin, J.; Tajkhorshid, E.; Schulten, K.; Chipot, C. Biophys. J. 2008, 94, 832-839
21. Wei, C.; Pohorille, A. J. Phys. Chem. B 2011, 115, 3681-3688
22. Türkcan, S.; Alexandrou, A.; Masson, J. Biophys. J. 2012, 102, 2288-2298
23. Ermak, D.; McCammon, J. J. Chem. Phys. 1978, 69, 1352
24. Best, R.; Hummer, G. Phys. Chem. Chem. Phys. 2011, 13, 16902-16911
25. Dose, V. Rep. Prog. Phys. 2003, 66, 1421
26. von Toussaint, U. Rev. Mod. Phys. 2011, 83, 943-999
27. MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L., Jr.; Evanseck, J.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, I. W. E.; Roux, B.; Schlenkrich, M.; Smith, J.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3586-3616
28. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten, K. J. Comput. Chem. 2005, 26, 1781-1802
29. Feller, S. E.; Zhang, Y. H.; Pastor, R. W.; Brooks, B. R. J. Chem. Phys. 1995, 103, 4613-4621
30. Miyamoto, S.; Kollman, P. A. J. Comput. Chem. 1992, 13, 952-962
31. Zhou, R. H.; Harder, E.; Xu, H. F.; Berne, B. J. J. Chem. Phys. 2001, 115
32. Batcho, P. F.; Case, D. A.; Schlick, T. J. Chem. Phys. 2001, 115, 4003-4018
33. Paterlini, M.; Ferguson, D. Chem. Phys. 1998, 236, 243-252
34. Lelièvre, T.; Rousset, M.; Stoltz, G. Nonlinearity 2008, 21, 1155
35. Allison, S.; McCammon, J. Biopolymers 1984, 23, 363-375
36. Burnecki, K.; Kepten, E.; Janczura, J.; Bronshtein, I.; Garini, Y.; Weron, A. Biophys. J. 2012, 103, 1839-1847
37. Weiss, M.; Elsner, M.; Kartberg, F.; Nilsson, T. Biophys. J. 2004, 87, 3518-3524
38. Glöckle, W.; Nonnenmacher, T. Biophys. J. 1995, 68, 46-53
39. Kou, S.; Xie, X. Phys. Rev. Lett. 2004, 93, 180603