Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models

ChemPhysChem

Volumn 8, Issue 3, 2007, Pages 452-461

  Baron, Riccardo ^a   Trzesniak, Daniel ^a   De Vries, Alex H ^a,b   Elsener, Andreas ^a   Marrink, Siewert J ^b   Van Gunsteren, Wilfred F ^a  

^a ETH ZURICH   (Switzerland)

^b UNIVERSITY OF GRONINGEN   (Netherlands)

Author keywords

Computational chemistry; Energy entropy compensation; Force field; GROMACS; GROMOS

Indexed keywords

COMPUTATIONAL CHEMISTRY; ENTROPY; HYDROCARBONS; IMPACT IONIZATION; MOLECULAR DYNAMICS; SOLVATION;

ATOMIC LEVEL SIMULATIONS; COARSE-GRAINED FORCE FIELDS; ENERGY-ENTROPY; ENTHALPY-ENTROPY COMPENSATION; FORCE FIELDS; GROMACS; GROMOS; MOLECULAR DYNAMICS SIMULATIONS;

ATOMS;

EID: 33847316387     PISSN: 14394235     EISSN: 14397641     Source Type: Journal    
DOI: 10.1002/cphc.200600658     Document Type: Article

References (76)

1. S. J. Marrink, A. H. de Vries, A. E. Mark, J. Phys. Chem. B 2004, 108, 750.
2. J. Baschnagel, K. Binder, P. Doruker, A. A. Gusev, O. Hahn, K. Kremer, W. L. Mattice, F. Müller-Plathe, M. Murat, W. Paul, S. Santos, U. W. Suter, V. Tries in Viscoelasticity, Atomistic Models, Statistical Chemistry, Vol 152, Advances in Polymer Sciences, Springer, Heidelberg, 2000, pp. 41-165.
3. F. Müller-Plathe, ChemPhysChem 2002, 3, 754.
4. K. Kremer, Macromol. Chem. Phys. 2003, 204, 257.
5. B. Smit, P. A. J. Hilbers, K. Esselink, L. A. M. Rupert, N. M. van Os, A. G. Schlijper, Nature 1990, 348, 624.
6. R. Goetz, R. Lipowsky, J. Chem. Phys. 1998, 108, 7397.
7. R. D. Groot, T. J. Madden, D. J. J. Tildesley, J. Chem. Phys. 1999, 110, 9739.
8. J. C. Shelley, M. Y. Shelley, R. C. Reeder, S. Bandyopadhyay, M. L. Klein, J. Phys. Chem. B 2001, 105, 4464.
9. M. Müller, K. Katsov, M. Schick, J. Polym. Sci. 2003, 41, 1441.
10. S. Izvekov, G. A. Voth, J. Chem. Theory Comput. 2006, 2, 637
11. J. C. Shillcock, R. Lipowsky, J. Phys. Condens. Matter 2006, 18, S1191.
12. V. Tozzini, Curr. Opin. Struct. Biol. 2005, 15, 144.
13. A. Y. Shih, A. Arkhipov, P. L. Freddolino, K. Schulten, J. Phys. Chem. B 2006, 110, 3674.
14. P. J. Bond, M. S. P. Sansom, J. Am. Chem. Soc. 2006, 128, 2697.
15. W. L. Jorgensen, D. S. Maxwell, J. Tirado-Rives, J. Am. Chem. Soc. 1996, 118, 11 225.
16. W. F. van Gunsteren, S. R. Billeter, A. A. Eising, P. H. Hünenberger, P. Krüger, A. E. Mark, W. R. P. Scott, I. G. Tironi, Biomolecular Simulation: The GROMOS96 Manual and User Guide, vdf Hochschulverlag AG an der ETH Zürich and BIOMOS b.v., Zürich, Groningen, 1996.
17. D. A. Case, T. E. Cheatham, T. Darden, H. Gohlke, R. Luo, K. M. Merz, A. Onufriev, C. Simmerling, B. Wang, R. J. Woods, J. Comput. Chem. 2005, 26, 1668.
18. W. F. van Gunsteren, X. Daura, A. E. Mark, Encycl. Comput. Chem. 1998, 2, 1211.
19. X. Daura, A. E. Mark, W. F. van Gunsteren, J. Comput. Chem. 1998, 19, 535.
20. L. D. Schuler, X. Daura, W. F. van Gunsteren, J. Comput. Chem. 2001, 22, 1205.
21. C. Oostenbrink, A. Villa, A. E. Mark, W. F. van Gunsteren, J. Comput. Chem. 2004, 25, 1656.
22. A. Ben-Naim, Solvation Thermodynamics, Plenum, New York, 1987.
23. N. F. A. van der Vegt, W. F. van Gunsteren, J. Phys. Chem. B 2004, 108, 1056.
24. D. Trzesniak, N. F. A. van der Vegt, W. F. van Gunsteren, Phys. Chem. Chem. Phys. 2004, 6, 697.
25. G. Graziano, J. Phys. Chem. B 2005, 109, 12 160.
26. N. S. Bodor, Z. Gabanyi, C.-K. Wong, J. Am. Chem. Soc. 1989, 111, 3783.
27. M. J. Warne, D. W. Connell, D. W. Hawker, G. Schueuermann, Chemosphere 1989, 19, 1113.
28. G. J. Niemi, S. C. Basak, G. D. Veith, G. Grunwald, Environ. Toxicol. Chem. 1992, 11, 893.
29. R. Faller, S. J. Marrink, Langmuir 2004, 20, 7686.
30. S. J. Marrink, A. E. Mark, Biophys. J. 2004, 87, 3894.
31. S. J. Marrink, J. Risselada, A. E. Mark, Chem. Phys. Lipids 2005, 135, 223.
32. R. Baron, A. H. de Vries, P. H. Hünenberger, W. F. van Gunsteren, J. Phys. Chem. B 2006, 110, 15 602.
33. R. Baron, A. H. de Vries, P. H. Hünenberger, W. F. van Gunsteren, J. Phys. Chem. B 2006, 110, 8464.
34. F. Reif in Fundamentals of Statistical and Thermal Physics, McGraw-Hill, Singapore, 1985, pp. 312-315.
35. J. W. Essex, C. A. Reynolds, W. G. Richards, J. Chem. Soc. Chem. Commun. 1989, 1152.
36. W. L. Jorgensen, J. M. Briggs, M. L. Contreras, J. Phys. Chem. 1990, 94, 1683.
37. D. L. Beveridge, F. M. DiCapua, Annu. Rev. Biophys. Biophys. Chem. 1989, 18, 431.
38. T. P. Straatsma, J. A. McCammon, Annu. Rev. Phys. Chem. 1992, 43, 407.
39. P. M. King in Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications, Vol. 2 (Eds.: W. F. van Gunsteren, P. K. Weiner, A. J. Wilkinson), Escom, Leiden, 1993, pp. 267-314.
40. P. Kollman, Chem. Rev. 1993, 93, 2395.
41. W. F. van Gunsteren, T. C. Beutler, F. Fraternali, P. M. King, A. E. Mark, P. E. Smith in Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications, Vol. 2 (Eds.: W. F. van Gunsteren, P. K. Weiner, A. J. Wilkinson), Escom, Leiden, 1993, pp. 315-348.
42. T. P. Straatsma in Reviews in Computational Chemistry, Vol. 9 (Eds.: K. B. Lipkowitz, D. B. Boyd), VCH, New York, 1996, pp. 81-127.
43. A. E. Mark, Encycl. Comput. Chem. 1998, 2, 1070.
44. w. P. Reinhardt, M. A. Miller, L. M. Amon, Acc. Chem. Res. 2001, 34, 607.
45. C. Chipot, D. A. Pearlman, Mol. Simul. 2002, 28, 1.
46. W. F. van Gunsteren, X. Daura, A. E. Mark, Helv. Chim. Acta 2002, 85, 3113.
47. B. Widom, J. Chem. Phys. 1963, 39, 2808.
48. B. Guillot, Y. Guissani, S. Bratos, J. Chem. Phys. 1991, 95, 3643.
49. B. Guillot, Y. Guissani, J. Chem. Phys. 1993, 99, 8075.
50. S. H. Fleischman, C. L. Brooks, J. Chem. Phys. 1987, 87, 3029.
51. W. F. van Gunsteren, D. Bakowies, R. Baron, I. Chandrasekhar, M. Christen, X. Daura, P. Gee, D. P. Geerke, A. Glättli, P. H. Hünenberger, M. A. Kastenholz, C. Oostenbrink, M. Schenk, D. Trzesniak, N. F. A. van der Vegt, H. B. Yu, Angew. Chem. 2006, 118, 4168-4198;
52. Angew. Chem. Int. Ed. 2006, 45, 4064-4092.
53. D. van der Spoel, A. R. van Buuren, M. E. F. Apol, P. J. Meulenhoff, D. P. Tieleman, A. L. T. M. Sijbers, B. Hess, K. A. Feenstra, E. Lindahl, R. van Drunen, H. J. C. Berendsen, GROMACS User Manual version 3.1.1, Nijenborgh 4, 9747 AG Groningen, The Netherlands, 2001. Internet: http://www.gromacs.org/.
54. M. Christen, P. H. Hünenberger, D. Bakowies, R. Baron, R. Bürgi, D. P. Geerke, T. N. Heinz, M. A. Kastenholz, V. Kräutler, C. Oostenbrink, C. Peter, D. Trzesniak, W. F. van Gunsteren, J. Comput. Chem. 2005, 26, 1719.
55. D. R. Lide, CRC Handbook of Chemistry and Physics, 72nd ed., CRC, Boca Raton, 1992.
56. K. Krynicki, C. D. Green, D. W. Sawyer, Faraday Discuss. Chem. Soc. 1978, 66, 199.
57. D. C. Douglass, D. W. Mccall, J. Phys. Chem. 1958, 62, 1102.
58. A. Ben-Naim, Y. Marcus, J. Chem. Phys. 1984, 81, 2016.
59. H.-A. Yu, M. Karplus, J. Chem. Phys. 1988, 89, 2366.
60. N. F. A. van der Vegt, D. Trzesniak, B. Kasumaj, W. F. van Gunsteren, ChemPhysChem 2004, 5, 144.
61. J. Hermans, A. Pathiaseril, A. Anderson, J. Am. Chem. Soc. 1988, 110, 5982.
62. A. Glättli, X. Daura, W. F. van Gunsteren, J. Comput. Chem. 2003, 24, 1087.
63. P. Schatzberg, J. Phys. Chem. 1963, 67, 776.
64. Vapour Pressures of Chemicals, Vol. 20 (Ed.: W. Martienssen) Landolt-Börnstein Series, Group IV, Springer, Darmstadt, 1999.
65. IUPAC Solubility Data Series (Ed.: J. W. Lorimer), Oxford University Press.
66. o = kT.
67. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, J. Hermans in Intermolecular Forces (Ed.: B. Pullman), D. Reidel Publishing Company, Dordrecht, 1981, pp. 331-342.
68. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. Di Nola, J. R. Haak, J. Chem. Phys. 1984, 81, 3684.
69. R. W. Hockney, Methods Comput. Phys. 1970, 9, 136.
70. I. G. Tironi, W. F. van Gunsteren, Mol. Phys. 1994, 83, 381.
71. D. Fincham, N. Quirke, D. J. Tildesley, J. Chem. Phys. 1986, 84, 4535.
72. T. C. Beutler, A. E. Mark, R. C. van Schaik, P. R. Gerber, W. F. van Gunsteren, Chem. Phys. Lett. 1994, 222, 529.
73. A. Villa, A. E. Mark, J. Comput. Chem. 2002, 23, 548.
74. C. Peter, C. Oostenbrink, A. van Dorp, W. F. van Gunsteren, J. Chem. Phys. 2004, 120, 2652.
75. E. Lindahl, B. Hess, D. van der Spoel, J. Mol. Model. 2001, 7, 306.
76. Using GROMACS versions 2.0 through to 3.2 the potentials and forces used in the codes are identical. Version 2.0 was used for the development of the CG force field.