Adaptive resolution molecular-dynamics simulation: Changing the degrees of freedom on the fly

Journal of Chemical Physics

Volumn 123, Issue 22, 2005, Pages

  Praprotnik, Matej ^a,b   Delle Site, Luigi ^a   Kremer, Kurt ^a  

^a MAX PLANCK INSTITUTE FOR POLYMER RESEARCH   (Germany)

^b NATIONAL INSTITUTE OF CHEMISTRY   (Slovenia)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; DEGREES OF FREEDOM (MECHANICS); MATHEMATICAL MODELS; OPTICAL RESOLVING POWER; STATISTICAL METHODS;

ADAPTIVE RESOLUTION; MOLECULAR SYSTEMS; MOLECULAR-DYNAMICS SIMULATION;

MOLECULAR DYNAMICS;

EID: 29144483372     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2132286     Document Type: Article

References (48)

1. Computational Molecular Dynamics: Challenges, Methods, Ideas, Lecture Notes in Computational Science and Engineering, Vol. 4, edited by, P. Deuflhard, J. Hermans, B. Leimkuhler, A. Mark, S. Reich, and, R. Skeel, (Springer Verlag, Berlin, 1999).
2. P. Minary, M. E. Tuckerman, and G. J. Martyna, Phys. Rev. Lett. 93, 150201 (2004).
3. D. Janežič, M. Praprotnik, and F. Merzel, J. Chem. Phys. 122, 174101 (2005).
4. M. Praprotnik and D. Janežič, J. Chem. Phys. 122, 174102 (2005).
5. M. Praprotnik and D. Janežič, J. Chem. Phys. 122, 174103 (2005).
6. M. Praprotnik, D. Janežič, and J. Mavri, J. Phys. Chem. A 108, 11056 (2004).
7. K. Kremer and F. Müller-Plathe, MRS Bull. 26, 205 (2001).
8. K. Kremer, in Multiscale Modeling and Simulation, Lecture Notes on Computational Science and Engineering, Vol. 39, edited by, S. Attinger, and, P. Koumoutsakis, (Springer, New York, 2004).
9. G. S. Ayton, H. L. Tepper, D. T. Mirijanian, and G. A. Voth, J. Chem. Phys. 120, 4074 (2004).
10. M. Kranenburg, M. Venturoli, and B. Smit, J. Phys. Chem. B 107, 11491 (2003).
11. S. O. Nielsen, C. F. Lopez, G. Srinivas, and M. L. Klein, J. Phys.: Condens. Matter 16, R481 (2004).
12. S. J. Marrink, A. H. de Vries, and A. E. Mark, J. Phys. Chem. B 108, 750 (2004).
13. R. Chang, G. S. Ayton, and G. A. Voth, J. Chem. Phys. 122, 244716 (2005).
14. I. R. Cooke, K. Kremer, and M. Deserno, Phys. Rev. E 72, 011506 (2005).
15. K. Kremer and G. S. Grest, J. Chem. Phys. 92, 5057 (1990).
16. W. Tschöp, K. Kremer, J. Batoulis, T. Bürger, and O. Hahn, Acta Polym. 49, 61 (1998).
17. W. Tschöp, K. Kremer, O. Hahn, J. Batoulis, and T. Bürger, Acta Polym. 49, 75 (1998).
18. R. Everaers, S. K. Sukumaran, G. S. Grest, C. Svaneborg, A. Sivasubramanian, and K. Kremer, Science 303, 823 (2004).
19. H. M. Chun, C. E. Padilla, D. N. Chin, J. Comput. Chem. 21, 159 (2000).
20. A. Malevanets and R. Kapral, J. Chem. Phys. 112, 7260 (2000).
21. E. Villa, A. Balaeff, and K. Schulten, Proc. Natl. Acad. Sci. U.S.A. 102, 6783 (2005).
22. L. Delle Site, C. F. Abrams, A. Alavi, and K. Kremer, Phys. Rev. Lett. 89, 156103 (2002).
23. C. F. Abrams, L. Delle Site, and K. Kremer, Phys. Rev. E 67, 021807 (2003).
24. L. Delle Site, S. Leon, and K. Kremer, J. Am. Chem. Soc. 126, 2944 (2004).
25. A. Laio, J. VandeVondele, and U. Roethlisberger, J. Chem. Phys. 116, 6941 (2002).
26. H. Rafii-Tabar, L. Hua, and M. Cross, J. Phys.: Condens. Matter 10, 2375 (1998).
27. J. Q. Broughton, F. F. Abraham, N. B. Bernstein, and E. Kaxiras, Phys. Rev. B 60, 2391 (1999).
28. J. A. Smirnova, L. V. Zhigilei, and B. J. Garrison, Comput. Phys. Commun. 118, 11 (1999).
29. G. Csanyi, T. Albaret, M. C. Payne, and A. D. Vita, Phys. Rev. Lett. 93, 175503 (2004).
30. C. F. Abrams, in Computational Soft Matter: From Synthetic Polymers to Proteins, edited by, N. Attig, K. Binder, H. Grubmüller, and, K. Kremer, NIC Series Vol. 23 (John von Neumann Institute for Computing, Bonn, 2004), pp. 275-288.
31. A. A. Louis, J. Phys.: Condens. Matter 14, 9187 (2002).
32. S. Curtarolo and G. Ceder, Phys. Rev. Lett. 88, 255504 (2002).
33. S. H. L. Klapp, D. J. Diestler, and M. Schoen, J. Phys.: Condens. Matter 16, 7331 (2004).
34. D. Reith, M. Pütz, and F. Müller-Plathe, J. Comput. Chem. 24, 1624 (2003).
35. G. Bryant, S. R. Williams, L. Qian, I. K. Snook, E. Perez, and F. Pincet, Phys. Rev. E 66, 060501 (R) (2002).
36. C. P. Lawrence and J. L. Skinner, Chem. Phys. Lett. 372, 842 (2003).
37. R. W. Zwanzig, J. Chem. Phys. 22, 1420 (1954).
38. A. R. Leach, Molecular Modeling, 2nd ed. (Pearson Education Limited, Harlow, 2001).
39. F. Schwabl, Quantum Mechanics, 2nd ed. (Springer-Verlag, Berlin, 1996).
40. T. Soddemann, B. Dünweg, and K. Kremer, Phys. Rev. E 68, 046702 (2003).
41. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Clarendon, Oxford, 1987).
42. H. Berendsen, J. Postma, W. V. Gunsteren, A. D. Nola, and J. Haak, J. Chem. Phys. 81, 3684 (1984).
43. B. A. Mann, R. Everaers, C. Holm, and K. Kremer, Europhys. Lett. 67, 786 (2004).
44. B. Dünweg and W. Paul, Int. J. Mod. Phys. C 2, 817 (1991).
45. http://www.espresso.mpg.de
46. A. Habenschuss, E. Johnson, and A. H. Narten, J. Chem. Phys. 74, 5234 (1981).
47. S. Leon, N. van der Vegt, L. Delle Site, and K. Kremer, Macromolecules 38, 5810 (2005).
48. W. Cai, M. de Koning, V. V. Bulatov, and S. Yip, Phys. Rev. Lett. 85, 3213 (2000).