Accuracy and convergence of free energy differences calculated from nonequilibrium switching processes

Journal of Computational Chemistry

Volumn 30, Issue 3, 2009, Pages 447-456

  Goette, Maik ^a   Grubmüller, Helmut ^a  

^a MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

Author keywords

Benchmark; Cgi; Crooks gaussian intersection; Fep; Free energy calculations; Gromaes; Molecular dynamics; Nonequilibrium simulations; Simulation; Thermodynamic integration

Indexed keywords

AMINO ACIDS; BENCHMARKING; MOLECULAR DYNAMICS; TEST FACILITIES;

CROOKS GAUSSIAN INTERSECTION; FREE-ENERGY CALCULATIONS; GROMAES; NON-EQUILIBRIUM SIMULATIONS; SIMULATION; THERMODYNAMIC INTEGRATION;

FREE ENERGY;

EID: 59849121675     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21073     Document Type: Article

References (55)

1. van Gunsteren, W. Protein Eng Des Select 1988, 2, 5.
2. Kollman, P. Chem Rev 1993, 93, 2395.
3. Rodinger, T.; Pomes, R. Curr Opin Struct Biol, 2005, 15, 164.
4. Shirts, M.; Mobley, D.; Chodera, J. Ann Rep Comp Chem 2007, 3, 41.
5. Jorgensen, W.; Ravimohan, C. J Chem Phys 1985, 83, 3050.
6. van Gunsteren, W; Daura, X.; Mark, A. Helvetica Chim Acta 2002, 85, 3113.
7. Hu, H.; Yun, R.; Hermans, J. Mol Simul 2002, 28, 67.
8. Lu, N.; Kofke, D.; Woolf, T. J Comput Chem 2004, 25, 28.
9. Woo, H.; Roux, B. Proc Natl Acad Sci 2005, 102, 6825.
10. Oostenbrink, C.; van Gunsteren, W. Chemistry(Weinheim) 2005, 11, 4340.
11. Oostenbrink, C.; van Gunsteren, W. Chem. Phys 2006, 323, 102.
12. Shirts, M.; Pande, V. J Chem. Phys 2005, 122, 144107.
13. Kofke, D. Mol Phys 2006, 104, 3701.
14. Mobley, D.; Chodera, J.; Dill, K. J Chem Phys 2006, 125, 084902.
15. Zwanzig, R. J Chem Phys 1954, 22, 1420.
16. Warshel, A.; Sussman, F. Proc Natl Acad Sci USA 1986, 83, 3806.
17. Hwang, J.; Warshel, A. Biochemistry 1987, 26, 2669.
18. Rao, S.; Singh, U.; Bash, P.; Kollman, P. Nature 1987, 328, 551.
19. Lu, N.; Kofke, D. J Chem Phys 2001, 114, 7303.
20. Lu, N.; Kofke, D. J Chem.Phys 2001, 115, 6866.
21. Lu, N.; Singh, J.; Kofke, D. J Chem Phys 2003, 118, 2977.
22. Kirkwood, J. J Chem Phys 1935, 3, 300.
23. Pearlman, D.; Kollman, P. J Chem Phys 1989, 91, 7831.
24. Straatsma, T.; McCammon, J. J Chem Phys 1991, 95, 1175.
25. Bennett, C. J Comput Phys 1976, 22, 245.
26. Jarzynski, C Phys Rev Lett 1997, 78, 2690.
27. Hendrix, D.; Jarzynski, C. J Chem Phys 2001, 114, 5974.
28. Lua, R.; Grosberg, A. J Phys Chem B 2005, 109, 6805.
29. Jarzynski, C. Phys Rev E 2006, 73, 46105.
30. Hummer, G. J Chem. Phys 2001, 114, 7330.
31. Crooks, G. J Statis Phys 1998, 90, 1481.
32. Shirts, M.; Bair, E.; Hooker, G.; Pande, V. Phys Rev Lett 2003, 91, 140601.
33. Shirts, M.; Pande, V. J Chem. Phys 2005, 122, 134508.
34. Beveridge, D.; DiCapua, F. Annu Rev Biophys Biophys Chem 1989, 18, 431.
35. Jarzynski, C Phys Rev E 1997, 56, 5018.
36. Straatsma, T.; McCammon, J. Ann Rev Phys Chem 1992, 43, 407.
37. Anderson, J. Biometrika 1972, 59, 19.
38. Crooks, G.; Jarzynski, C Phys Rev E 2007, 75, 21116.
39. Massey, F. Jr, J Am. Stat Assoc 1951, 46, 68.
40. Kosztin, I.; Barz, B.; Janosi, L. J Chem Phys 2006, 124, 064106.
41. Atkinson, K. An Introduction to Numerical Analysis; Wiley: New York, 1978.
42. Hess, B. J Chem. Phys 2002, 116, 209.
43. Jorgensen, W.; Maxwell, D.; Tirado-Rives, J. Am Chem. Soc 1996, 118, 11225.
44. Strasser, A.; Dickmanns, A.; Luhrmann, R.; Ficner, R. EMBO J 2005, 24, 2235.
45. Wang, J.; Cieplak, P.; Kollman, P. J Comput Chem 2000, 21, 1049.
46. Sorin, E.; Pande, V. Biophys J 2005, 88, 2472.
47. Aduri, R.; Psciuk, B.; Saro, P.; Taniga, H.; Schlegel, H.; SantaLucia, J. Jr J Chem. Theory Comput 2007, 3, 1464.
48. Meagher, K.; Redman, L.; Carlson, H. J Comput Chem 2003, 24, 1016.
49. Darden, T.; York, D.; Pedersen, L. J Chem Phys 1993, 98, 10089.
50. Berendsen, H.; Postma, J.; van Gunsteren, W.; DiNoIa, A.; Haak, J. J Chem. Phys 1984, 81, 3684.
51. Jorgensen, W; Chandrasekhar, J.; Madura, J.; Impey, R.; Klein, M. J Chem Phys 1983, 79, 926.
52. van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A.; Berendsen, H. J Comput Chem 2005, 26, 1701.
53. Beutler, T.; Mark, A.; van Schaik, R.; Gerber, P.; van Gunsteren, W. Chem Phys Lett 1994, 222, 529.
54. Ben-Naim, A.; Marcus, Y. J Chem Phys 1984, 81, 2016.
55. Huber, J.; Cronshagen, U.; Kadokura, M.; Marshallsay, C.; Wada, T.; Sekine, M.; Lührmann, R. EMBO J 1998, 17, 4114.