Optimization of coarse-grained interaction potential: Inside inherent limitations of coarse-graining methods

Journal of Physical Chemistry B

Volumn 115, Issue 21, 2011, Pages 6985-6994

  Kowalczyk, Piotr ^a   Gauden, Piotr A ^b   Ciach, Alina ^c  

^a CURTIN UNIVERSITY   (Australia)

^b NICOLAUS COPERNICUS UNIVERSITY   (Poland)

^c INSTITUTE OF PHYSICAL CHEMISTRY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

ACETONE; BENZENE; CARBON DIOXIDE; LIQUIDS; METHANOL; TOLUENE;

APROTIC; APROTIC LIQUIDS; COARSE-GRAINED; COARSE-GRAINING METHOD; COHESIVE PROPERTY; DIRECTIONAL INTERACTIONS; EQUILIBRIUM PROPERTIES; INHERENT LIMITATIONS; INTERACTION POTENTIALS; INTERFACIAL PROPERTY; MOLECULAR HYDROGEN; VAPOR-LIQUID;

OPTIMIZATION;

EID: 79957625979     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp2019999     Document Type: Article

References (47)

1. Cheatham, T. E., III. Annu. Rep. Comput. Chem. 2005, 1, 75
2. Levy, Y.; Onuchic, J. N. Annu. Rev. Biophys. Biomol. Struct. 2006, 35, 389
3. Okazaki, K.-I.; Koga, N.; Takada, S.; Onuchic, J. N.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 11844
4. Comer, J.; Dimitrov, V.; Zhao, Q.; Timp, G.; Aksimentiev, A. Biophys. J. 2009, 96, 593
5. Voth, G. A. In Coarse-Graining of Condensed Phase and Biomolecular Systems; Voth, G. A., Ed.; CRC Press: Boca Raton, FL, 2008.
6. Lyubartsev, A.; Mirzoev, A.; Chen, L. J.; Laaksonen, A. Faraday Discuss. 2010, 144, 43
7. Marrink, S. J.; Risselada, H. J.; Yefimov, S.; Tieleman, D. P.; de Vries, A. H. J. Phys. Chem. B 2007, 111, 7812
8. Izvekov, S.; Voth, G. A. J. Phys. Chem. B 2005, 109, 2469
9. Izvekov, S.; Parrinello, M.; Burnham, C. J.; Voth, G. A. J. Chem. Phys. 2004, 120, 10896
10. Hooper, J. B.; Bedrov, D.; Smith, G. D. Phys. Chem. Chem. Phys. 2009, 11, 2034
11. Reith, D.; Meyer, H.; Müller-Plathe, F. Comput. Phys. Commun. 2002, 148, 299
12. Reith, D.; Pütz, M.; Müller-Plathe, F. J. Comput. Chem. 2003, 24, 1624
13. Lyubartsev, A. P. Eur. Biophys. J. 2005, 35, 53
14. Lyubartsev, A. P.; Karttunen, M.; Vattulainen, I.; Laaksonen, A. Soft Mater. 2003, 1, 121
15. Tòth, G. J. Phys.: Condens. Matter 2007, 19, 335220
16. Chaimovich, A.; Shell, M. S. Phys. Chem. Chem. Phys. 2009, 11, 1901
17. Kamio, K.; Moorthi, K.; Theodorou, D. N. Macromolecules 2007, 40, 710
18. Ercolessi, F.; Adams., J. B. Europhys. Lett. 1994, 26, 583
19. Ercolessi, F.; Parrinello, M.; Tosatti, E. Philos. Mag. A 1988, 58, 213
20. Izvekov, S.; Voth, G. A. J. Chem. Phys. 2005, 123, 134105
21. Izvekov, S.; Chung, P. W.; Rice, B. M. J. Chem. Phys. 2010, 133, 064109
22. Noid, W. G.; Chu, J.-W.; Ayton, G. S.; Krishna, V.; Izvekov, S.; Voth, G. A.; Das, A.; Andersen, H. C. J. Chem. Phys. 2008, 128, 244114
23. Noid, W. G.; Liu, P.; Wang, Y.; Chu, J.-W.; Ayton, G. S.; Izvekov, S.; Andersen, H. S.; Voth, G. A. J. Chem. Phys. 2008, 128, 244115
24. Chu, J. W.; Ayton, G. S.; Izvekov, S.; Voth, G. A. Mol. Phys. 2007, 105, 167
25. Kowalczyk, P.; Gauden, P. A.; Ciach, A. J. Phys. Chem. B 2009, 113, 12988
26. Sakai, H.; Stillinger, F. H.; Torquato, S. J. Chem. Phys. 2002, 117, 297
27. Wick, C. D.; Siepmann, J. I.; Klotz, W. L.; Schureb, M. R. J. Chromatogr., A 2002, 954, 181
28. Jorgensen, W. L.; Jenson, C. J. Comput. Chem. 1998, 19, 1179
29. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225
30. Nguyen, T. X. Characterization of Nanoporous Carbons. Ph.D. Thesis, The University of Queensland, Brisbane, Australia, 2006.
31. Kowalczyk, P.; Furmaniak, S.; Gauden, P. A.; Terzyk, A. P. J. Phys. Chem. C 2010, 114, 21465
32. Belof, J. L.; Stern, A. C.; Space, B. J. Chem. Theory Comput. 2008, 4, 1332
33. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Clarendon: Oxford, U.K., 1987.
34. Frenkel, D.; Smit, B. Understanding Molecular Simulation From Algorithms To Applications; Academic Press: London, 1996.
35. Kowalczyk, P.; Ciach, A.; Neimark, A. V. Langmuir 2008, 24, 6603
36. Kowalczyk, P.; Holyst, R.; Terrones, M.; Terrones, H. Phys. Chem. Chem. Phys. 2007, 9, 1786
37. Hill, T. L. Introduction to Statistical Mechanics; Dover: New York, 1986.
38. Jang, S. S.; Lin, S.-T.; Maiti, P. K.; Blanco, M.; Goddard, W. A.; Shuler, P.; Tang, Y. J. Phys. Chem. B 2004, 108, 12130
39. Rowlinson, J. S.; Widom, B. Molecular Theory of Capillarity; Clarendon: Oxford, U.K., 1982.
40. Biscay, F.; Ghoufi, A.; Goujon, F.; Lachet, V.; Malfreyt, P. J. Chem. Phys. 2009, 130, 184710
41. Kirkwood, J. G.; Buff, F. P. J. Chem. Phys. 1949, 17, 338
42. Alejandre, J.; Tildesley, D. J.; Chapela, G. A. J. Chem. Phys. 1995, 102, 4574
43. Silvera, I. F.; Goldman, V. J. Chem. Phys. 1978, 69, 4209
44. Kowalczyk, P.; Hołyst, R.; Terzyk, A. P.; Gauden, P. A. Langmuir 2006, 22, 1970
45. Kowalczyk, P.; Tanaka, H.; Hołyst, R.; Kaneko, K.; Ohmori, T.; Miyamoto, J. J. Phys. Chem. B 2005, 109, 17174
46. Kowalczyk, P.; Gauden, P. A.; Terzyk, A. P. J. Phys. Chem. B 2008, 112, 8275
47. Kowalczyk, P.; Gauden, P. A.; Terzyk, A. P.; Furmaniak, S. Phys. Chem. Chem. Phys. 2010, 12, 11351