Versatile object-oriented toolkit for coarse-graining applications

Journal of Chemical Theory and Computation

Volumn 5, Issue 12, 2009, Pages 3211-3223

  Rühle, Victor ^a   Junghans, Christoph ^a   Lukyanov, Alexander ^a   Kremer, Kurt ^a   Andrienko, Denis ^a  

^a MAX PLANCK INSTITUTE FOR POLYMER RESEARCH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 73949097591     PISSN: 15499618     EISSN: None     Source Type: Journal    
DOI: 10.1021/ct900369w     Document Type: Article

References (66)

1. Tschöp, W.; Kremer, K.; Batoulis, J.; Burger, T.; Hahn, O. Acta Polym. 1998, 49, 61-74.
2. Shelley, J.; Shelley, M.; Reeder, R.; Bandyopadhyay, S.; Klein, M. J. Phys. Chem. B 2001, 105, 4464-4470.
3. Abrams, C.; Kremer, K. Macromolecules 2003, 36, 260-267.
4. Murtola, T.; Falck, E.; Patra, M.; Karttunen, M.; Vattulainen, I. J. Chem. Phys. 2004, 121, 9156-9165.
5. Izvekov, S.; Voth, G. J. Chem. Phys. 2005, 123, 134105.
6. Sun, Q.; Faller, R. J.Chem. Theo. Comp. 2006, 2, 607-615.
7. Harmandaris, V.; Adhikari, N.; van der Vegt, N.; Kremer, K. Macromolecules 2006, 39, 6708-6719.
8. Yelash, L.; Müller, M.; Wolfgang, P.; Binder, K. J. Chem. Theor. Comp. 2006, 2, 588-597.
9. Shih, A.; Arkhipov, A.; Freddolino, P.; Schulten, K. J. Phys. Chem. B 2006, 110, 3674-3684.
10. Lyubartsev, A.; Eur. Biophys. J. 2005, 35, 53-61.
11. Zhou, J.; Thorpe, I.; Izvekov, S.; Voth, G. Biophys. J. 2007, 92, 4289-4303.
12. Villa, A.; van der Vegt, N.; Peter, C. Phys. Chem. Chem. Phys. 2009, 11, 2068-2076.
13. Ercolessi, F.; Adams, J. B. Europhys. Lett. 1994, 26, 583- 588.
14. Hess, B.; Holm, C.; van der Vegt, N. Phys. Rev. Lett. 2006, 96, 147801.
15. Reith, D.; Pütz, M.; Müller-Plathe, F. J. Comput. Chem. 2003, 24, 1624-1636.
16. Lyubartsev, A.; Laaksonen, A. Phys. Rev. E: Stat. Phys., Plasmas, Fluids, Relat. Interdiscip. Top. 1995, 52, 3730- 3737.
17. Soper, A. Chem. Phys. 1996, 202, 295-306.
18. Izvekov, S.; Parrinello, M.; Burnham, C. J.; Voth, G. A. J. Chem. Phys. 2004, 120, 10896-10913.
19. Toth, G. J. Phys. Cond. Mat. 2007, 19, 335222.
20. Baschnagel, J.; Binder, K.; Doruker, P.; Gusev, A. A.; Hahn, O.; Kremer, K.; Mattice, W. L.; Müller-Plathe, F.; Murat, M.; Paul, W.; Santos, S.; Suter, U. W.; Tries, V. Advances in Polymer Science: Viscoelasticity, Atomistic Models, Statistical Chemistry; Springer Verlag: Heidelberg, Germany, 2000.
21. Kremer, K.In Soft and fragile matter, nonequilibrium dynamics, metastability and flow; Cates, M. E., Evans, M. R., Eds.; J. W. Arrowsmith Ltd.: Bristol, U.K., 2000.
22. Müller-Plathe, F. Chem. Phys. Phys. Chem. 2002, 3, 754- 769.
23. Johnson, M.; Head-Gordon, T.; Louis, A. J. Chem. Phys. 2007, 126, 144509.
24. Coarse-Graining of Condensed Phase and Biomolecular Systems; Voth, G. A., Ed.; CRC Group: Boca Raton, FL, 2008.
25. Murtola, T.; Bunker, A.; Vattulainen, I.; Deserno, M.; Karttunen, M. Phys. Chem. Chem. Phys. 2009, 11, 1869-1892.
26. Peter, C.; Kremer, K. Soft Matter 2009, accepted. DOI: 10.1039/b912027k.
27. Henderson, R. Phys. Lett. A 1974, A49, 197-198.
28. Chayes, J.; Chayes, L. J. Stat. Phys. 1984, 36, 471-488.
29. Chayes, J.; Chayes, L.; Lieb, E. Comm. Math. Phys. 1984, 93, 57-121.
30. Leon, S.; van der Vegt, N.; Delle Site, L.; Kremer, K. Macromolecules 2005, 38, 8078-8092.
31. Junghans, C.; Praprotnik, M.; Kremer, K. Soft Matter 2008, 4, 156-161.
32. Wang, H.; Junghans, C.; Kremer, K. Eur. Phys. J. E 2009, 28, 221-229.
33. Murtola, T.; Falck, E.; Karttunen, M.; Vattulainen, I. J. Chem. Phys. 2007, 126, 075101.
34. Noid, W.; Chu, J.; Ayton, G.; Voth, G. J. Phys. Chem. B 2007, 111, 4116-4127.
35. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. J. Chem. Theo. Comp. 2008, 4, 435-447.
36. Nezbeda, I.; Slovak, J. Mol. Phys. 1997, 90, 353-372.
37. Wallqvist, A.; Mountain, R. D. Rev. Comp. Chem. 2007, 13, 183-247.
38. Kusalik, P. G.; Svishchev, I. M. Science 1994, 65, 1219-1221.
39. Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. J. Phys. Chem. 1987, 91, 6269-6271.
40. Berendsen, H. J. C.; Postma, J. P. M.; Vangunsteren, W. F.; Dinola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690.
41. Gunsteren, W. F. V.; Berendsen, H. J. C. Mol. Sim. 1988, 1, 173.
42. Noid, W. G.; Liu, P.; Wang, Y.; Chu, J.; Ayton, G.; Izvekov, S.; Andersen, H. C.; Voth, G. J. Chem. Phys. 2008, 128, 244115.
43. Janke, W. Statistical Analysis of Simulations: Data Correlations and Error Estimation, Lecture notes; Grotendorst, J., Marx, D., Muramatsu, A., Eds.; John von Neumann Institut für Computing (NIC) Series, Vol. 10; NIC: Jülich, Germany, 2002; pp 423-445.
44. Jorgensen, W.; Tirado-Rives, J. J. Chem. Soc., Abstr. 1998, 216, U696-U696.
45. Jorgensen, W.; Tirado-Rives, J. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6665-6670.
46. Nosé, S. Mol. Phys. 1984, 52, 255-268.
47. Hoover, W. G. Phys. Rev. A: At., Mol., Opt. Phys. 1985, 31, 1695.
48. Bussi, G.; Donadio, D.; Parrinello, M. J. Chem. Phys. 2007, 126, 014101.
49. Kirkpatrick, J.; Marcon, V.; Nelson, J.; Kremer, K.; Andrienko, D. Phys. Rev. Lett. 2007, 98, 227402.
50. Feng, X.; Marcon, V.; Pisula, W.; Hansen, M.; Kirkpatrick, J.; Grozema, F.; Andrienko, D.; Kremer, K.; Müllen, K. Nat. Mat. 2009, 8, 421-426.
51. Golub, G. H.; Van Loan, C. F. Matrix Computations, 3rd ed.; Johns Hopkins University Press: Baltimore, MD, 1996.
52. Harmandaris, V. A.; Reith, D.; Van der Vegt, N. F. A.; Kremer, K. Macromol. Chem. Phys. 2007, 208, 2109-2120.
53. Villa, A.; Peter, C.; van der Vegt, N. F. A. Phys. Chem. Chem. Phys. 2009, 11, 2077-2086.
54. Noid, W. G.; Chu, J.; Ayton, G. S.; Krishna, V.; Izvekov, S.; Voth, G.; Das, A.; Andersen, H. C. J. Chem. Phys. 2008, 128, 244114.
55. See also footnote 65.
56. j} which are obtained from an atomistic trajectory shall not be confused with the coordinates of a trajectory obtained from coarse-grained simulations
57. Note that here we only consider the special case of a linear relation between the r and R. M is a block-diagonal matrix and to construct it is enough to specify building blocks for each molecule type. For polymers it is enough to specify M for one repeat unit only.
58. Note that this is often a "special" trajectory which is designed to decouple the degrees of freedom of interest, e. g., a single polymer chain in vacuum with appropriate exclusions.
59. Note that, as before, we ignored an irrelevant normalization prefactor Z.
60. 52,53 The concept is illustrated in section IV for liquid propane and a single molecule of hexane.
61. 2), which is the potential of mean force, eq 2.
62. A formal statistical mechanical framework of force matching applied to a liquid state, or a multiscale coarse-graining method, is given in ref 54.
63. http://www.espresso-pp.de.
64. αβ systematically change with the box size.
65. 44,45 The latter models map the potentials, which are analytical functions of bonds, angles, and dihedral Coarse-Graining Applications J. Chem. Theory Comput., Vol. 5, No. 12, 2009 3223 dynamic properties of the corresponding substances. In our case coarse-grained potentials are tabulated functions of coarse-grained variables and only the mapping (hydrogens embedded into heavier atoms) is similar to that of the united atom force-fields.
66. For condensed phase systems, the error introduced by the off-plane component of the force might be compensated by some other pair interactions. In this particular case, however, coarse-graining of liquid hexane with both bonded and non-bonded degrees of freedom treated simultaneously results in a very similar angular distribution to that of a single molecule in vacuum.