Adaptive Switching of Interaction Potentials in the Time Domain: An Extended Lagrangian Approach Tailored to Transmute Force Field to QM/MM Simulations and Back

Journal of Chemical Theory and Computation

Volumn 11, Issue 6, 2015, Pages 2429-2439

  Böckmann, Marcus ^a   Doltsinis, Nikos L ^a   Marx, Dominik ^b  

^a UNIVERSITY OF MÜNSTER   (Germany)

^b RUHR UNIVERSITY BOCHUM   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84931261047     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/acs.jctc.5b00142     Document Type: Article

References (53)

1. Marx, D., Hutter, J. Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods; Cambridge University Press: Cambridge, 2009.
2. Warshel, A.; Levitt, M. J. Mol. Biol. 1976, 103, 227-249
3. Gao, J. In Reviews in Computational Chemistry; Lipkowitz, K. B.; Boyd, D. B., Eds.; VCH: New York, 1995; Vol. 7; pp 119-185.
4. Senn, H. M.; Thiel, W. Angew. Chem., Int. Ed. 2009, 48, 1198-1229
5. Grotendorst, J.; Attig, N.; Blügel, S.; Marx, D., Eds. Multiscale Simulation Methods in Molecular Sciences; Forschungszentrum Jülich: Jülich, Germany, 2009.
6. Poma, A. B.; Delle Site, L. Phys. Rev. Lett. 2010, 104, 250201-1-250201-4
7. Böckmann, M.; Marx, D.; Peter, C.; Delle Site, L.; Kremer, K.; Doltsinis, N. L. Phys. Chem. Chem. Phys. 2011, 13, 7604-7621
8. Grotendorst, J.; Sutmann, G.; Gompper, G.; Marx, D., Eds. Hierarchial Methods for Dynamics in Complex Molecular Systems; Forschungszentrum Jülich: Jülich, Germany, 2012.
9. Wassenaar, T. A.; Ingolfsson, H. I.; Prieß, M.; Marrink, S. J.; Schäfer, L. V. J. Phys. Chem. B 2013, 117, 3516-3530
10. Karplus, M. Angew. Chem., Int. Ed. 2014, 53, 9992-10005
11. Kalli, A. C.; Sansom, M. S. P. Biochem. Soc. Trans. 2014, 42, 1418-1424
12. Potestio, R.; Peter, C.; Kremer, K. Entropy 2014, 16, 4199-4245
13. Delle Site, L. Entropy 2014, 16, 23-40
14. Kerdcharoen, T.; Liedl, K. R.; Rode, B. M. Chem. Phys. 1996, 211, 313-323
15. Schwenk, C. F.; Loeffler, H. H.; Rode, B. M. J. Am. Chem. Soc. 2003, 125, 1618-1624
16. Hofer, T. S.; Pribil, A. B.; Randolf, B. R.; Rode, B. M. J. Am. Chem. Soc. 2005, 127, 14231-14238
17. Kerdcharoen, T.; Morokuma, K. Chem. Phys. Lett. 2002, 355, 257-262
18. Heyden, A.; Lin, H.; Truhlar, D. G. J. Phys. Chem. B 2007, 111, 2231-2241
19. Pezeshki, S.; Lin, H. J. Chem. Theory Comput. 2011, 7, 3625-3634
20. Pezeshki, S.; Davis, C.; Heyden, A.; Lin, H. J. Chem. Theory Comput. 2014, 10, 4765-4776
21. Bulo, R. E.; Ensing, B.; Sikkema, J.; Visscher, L. J. Chem. Theory Comput. 2009, 5, 2212-2221
22. Nielsen, S. O.; Moore, P. B.; Ensing, B. Phys. Rev. Lett. 2010, 105, 237802-1-237802-4
23. Waller, M. P.; Kumbhar, S.; Yang, J. ChemPhysChem 2014, 15, 3218-3225
24. Csányi, G.; Albaret, T.; Payne, M.; De Vita, A. Phys. Rev. Lett. 2004, 93, 175503-1-175503-4
25. Rafii-Tabar, H.; Hua, L.; Cross, M. J. Phys. Cond. Mater. 1998, 10, 2375-2387
26. Smirnova, J. A.; Zhigilei, L. V.; Garrison, B. J. Comput. Phys. Commun. 1999, 118, 11-16
27. Broughton, J. Q.; Abraham, F. F.; Bernstein, N.; Kaxiras, E. Phys. Rev. B 1999, 60, 2391-2403
28. Praprotnik, M.; Delle Site, L.; Kremer, K. J. Chem. Phys. 2005, 132, 224106-1-224106-17
29. Wang, H.; Schütte, C.; Delle Site, L. J. Chem. Theory Comput. 2012, 8, 2878-2887
30. Fritsch, S.; Poblete, S.; Junghans, C.; Ciccotti, G.; Delle Site, L.; Kremer, K. Phys. Rev. Lett. 2012, 108, 170602-1-170602-5
31. Wang, H.; Hartmann, C.; Schütte, C.; Delle Site, L. Phys. Rev. X 2013, 3, 011018-1-011018-16
32. Agarwal, A.; Wang, H.; Schütte, C.; Delle Site, L. J. Chem. Phys. 2014, 141, 034102-1-034102-12
33. Ensing, B.; Nielsen, S. O.; Moore, P. B.; Klein, M. L.; Parrinello, M. J. Chem. Theory Comput. 2007, 3, 1100-1105
34. Praprotnik, M.; Poblete, S.; Delle Site, L.; Kremer, K. Phys. Rev. Lett. 2011, 107, 099801-1-099801-2
35. Nielsen, S. O.; Moore, P. B.; Ensing, B. Phys. Rev. Lett. 2011, 107, 099802
36. Potestio, R.; Fritsch, S.; Español, P.; Delgado-Buscalioni, R.; Kremer, K.; Everaers, R.; Donadio, D. Phys. Rev. Lett. 2013, 110, 108301-1-108301-5
37. Delle Site, L. Phys. Rev. E 2007, 76, 047701-1-047701-4
38. Grossfield, A. Biochim. Biophys. Acta 2011, 1808, 1868-1878
39. Johnston, J. M.; Filizola, M. Curr. Opin. Struct. Biol. 2011, 21, 552-558
40. Feringa, B. L.; Browne, R. W., Eds. Molecular Switches; Wiley-VCH: Weinheim, Germany, 2011.
41. Gao, J. J. Phys. Chem. 1992, 96, 537-540
42. Gao, J.; Xia, X. Science 1992, 258, 631-635
43. Abrams, J. B.; Rosso, L.; Tuckerman, M. E. J. Chem. Phys. 2006, 125, 074115-1-074115-12
44. Hutter, J. Car-Parrinello Molecular Dynamics: An Ab Initio Electronic Structure and Molecular Dynamics Program. www.cpmd.org, (accessed Aug 2014).
45. Becke, A. D. Phys. Rev. A 1988, 38, 3098-3100
46. Lee, C.; Yang, W.; Parr, R. C. Phys. Rev. B 1988, 37, 785-789
47. Nosé, S. J. Chem. Phys. 1984, 81, 511-519
48. Hoover, W. G. Phys. Rev. A 1985, 31, 1695-1697
49. Martyna, G. J.; Klein, M. L.; Tuckerman, M. E. J. Chem. Phys. 2002, 97, 2635-2643
50. Tuckerman, M. E. Statistical Mechanics: Theory and Molecular Simulation; Oxford University Press: New York, 2010.
51. Böckmann, M.; Peter, C.; Delle Site, L.; Doltsinis, N. L.; Kremer, K.; Marx, D. J. Chem. Theory Comput. 2007, 3, 1789-1802
52. Perdew, J. P.; Burke, K.; Ernzerhof, M. Phys. Rev. Lett. 1996, 77, 3865-3868
53. Perdew, J. P.; Burke, K.; Ernzerhof, M. Phys. Rev. Lett. 1997, 78, 1396