Investigation of coarse-grained mappings via an iterative generalized Yvon-Born-Green method

Journal of Physical Chemistry B

Volumn 118, Issue 28, 2014, Pages 8295-8312

  Rudzinski, Joseph F ^a   Noid, William G ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; CONFORMATIONS; MAPPING; MOLECULES;

COARSE GRAINING; COMPLEX MOLECULES; CROSS-CORRELATIONS; EFFICIENT SIMULATION; MOLECULAR CONFORMATION; PREDICTIVE ANALYSIS; RADIAL DISTRIBUTION FUNCTIONS; THEORETICAL FRAMEWORK;

ITERATIVE METHODS;

EID: 84904540490     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp501694z     Document Type: Article

References (92)

1. Schlick, T.; Collepardo-Guevara, R.; Halvorsen, L. A.; Jung, S.; Xiao, X. Biomolecular modeling and simulation: a field coming of age Q. Rev. Biophys. 2011, 44, 191-228
2. Voth, G. A., Ed. Coarse-graining of condensed phase and biomolecular systems; CRC Press: Boca Raton, FL, USA, 2009.
3. Nielsen, S. O.; Lopez, C. F.; Srinivas, G.; Klein, M. L. Coarse grain models and the computer simulation of soft materials J. Phys.: Condens. Matter 2004, 16, R481
4. Ayton, G. S.; Noid, W. G.; Voth, G. A. Multiscale Modeling of biomolecular systems: In serial and in parallel Curr. Opin. Struc. Biol. 2007, 17, 192-198
5. Guenza, M. G. Theoretical models for bridging timescales in polymer dynamics. J. Phys.: Condens. Matter 2008, 20.
6. Murtola, T.; Bunker, A.; Vattulainen, I.; Deserno, M.; Karttunen, M. Multiscale modeling of emergent materials: Biological and soft matter Phys. Chem. Chem. Phys. 2009, 11, 1869-1892
7. Peter, C.; Kremer, K. Multiscale simulation of soft matter systems Faraday Discuss. 2010, 144, 9-24
8. Takada, S. Coarse-grained molecular simulations of large biomolecules Curr. Opin. Struc. Biol. 2012, 22, 130-137
9. Riniker, S.; Allison, J. R.; van Gunsteren, W. F. On developing coarse-grained models for biomolecular simulation: A review Phys. Chem. Chem. Phys. 2012, 14, 12423-12430
10. Karimi-Varzaneh, H. A.; Müller-Plathe, F. Coarse-grained modeling for macromolecular chemistry Top. Curr. Chem. 2012, 307, 295-321
11. Brini, E.; Algaer, E. A.; Ganguly, P.; Li, C.; Rodriguez-Ropero, F.; van der Vegt, N. F. A. Systematic coarse-graining methods for soft matter simulations-a review Soft Matter 2013, 9, 2108-2119
12. Ingólfsson, H. I.; Lopez, C. A.; Uusitalo, J. J.; de Jong, D. H.; Gopal, S. M.; Periole, X.; Marrink, S. J. The power of coarse graining in biomolecular simulations Wiley Interdiscip. Rev. Comput. Mol. Sci. 2014, 4 (3) 225-228
13. Noid, W. G. Perspective: Coarse-grained models for biomolecular systems J. Chem. Phys. 2013, 139, 090901
14. Saunders, M. G.; Voth, G. A. Coarse-Graining Methods for Computational Biology Annu. Rev. Biophys. 2013, 42, 73-93
15. Shelley, J. C.; Shelley, M. Y.; Reeder, R. C.; Bandyopadhyay, S.; Klein, M. L. A coarse grain model for phospholipid simulation J. Phys. Chem. B 2001, 105, 4464-4470
16. Shinoda, W.; Devane, R.; Klein, M. L. Multi-property fitting and parameterization of a coarse grained model for aqueous surfactants Mol. Sim. 2007, 33, 27-36
17. Marrink, S. J.; de Vries, A. H.; Mark, A. E. Coarse grained model for semiquantitative lipid simulations J. Phys. Chem. B 2004, 108, 750-760
18. Marrink, S. J.; Risselada, H. J.; Yefimov, S.; Tieleman, D. P.; de Vries, A. H. The MARTINI force field: Coarse grained model for biomolecular simulations J. Phys. Chem. B 2007, 111, 7812-7824
19. Müller-Plathe, F. Coarse-graining in polymer simulation: From the atomistic to the mesoscopic scale and back ChemPhysChem 2002, 3, 754-769
20. Lyubartsev, A. P.; Laaksonen, A. Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach Phys. Rev. E 1995, 52, 3730-3737
21. Kirkwood, J. G. Statistical mechanics of fluid mixtures J. Chem. Phys. 1935, 3, 300-313
22. Liwo, A.; Oldziej, S.; Pincus, M. R.; Wawak, R. J.; Rackovsky, S.; Scheraga, H. A. A united-residue force field for off-lattice protein-structure simulations. 1. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data J. Comput. Chem. 1997, 18, 849-873
23. Noid, W. G.; Chu, J.-W.; Ayton, G. S.; Krishna, V.; Izvekov, S.; Voth, G. A.; Das, A.; Andersen, H. C. The Multiscale Coarse-graining Method. I. A Rigorous Bridge between Atomistic and Coarse-grained Models J. Chem. Phys. 2008, 128, 244114
24. Liwo, A.; Czaplewski, C.; Pillardy, J.; Scheraga, H. A. Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field J. Chem. Phys. 2001, 115, 2323-2347
25. Noid, W. G. Systematic methods for structurally consistent coarse-grained models Methods Mol. Biol. 2013, 924, 487-531
26. Savelyev, A.; Papoian, G. A. Chemically accurate coarse graining of double-stranded DNA Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 20340-20345
27. Schommers, W. Pair potentials in disordered many-particle systems: A study of liquid gallium Phys. Rev. A 1983, 28, 3599-3605
28. Reatto, L.; Levesque, D.; Weis, J. J. Iterative predictor-corrector method for extraction of the pair interaction from structural data for dense classical liquids Phys. Rev. A 1986, 33, 3451-3465
29. Soper, A. K. Empirical potential Monte Carlo simulation of fluid structure Chem. Phys. 1996, 202, 295-306
30. Lyubartsev, A.; Mirzoev, A.; Chen, L. J.; Laaksonen, A. Systematic coarse-graining of molecular models by the Newton inversion method Faraday Discuss. 2010, 144, 43-56
31. Murtola, T.; Falck, E.; Patra, M.; Karttunen, M.; Vattulainen, I. Coarse-grained model for phospholipid/cholesterol bilayer J. Chem. Phys. 2004, 121, 9156-9165
32. Lyubartsev, A. P. Multiscale modeling of lipids and lipid bilayers Eur. Biophys. J. 2005, 35, 53-61
33. Lyubartsev, A. P.; Laaksonen, A. Osmotic and activity coefficients from effective potentials for hydrated ions Phys. Rev. E 1997, 55, 5689-5696
34. Savelyev, A.; Papoian, G. A. Molecular renormalization group coarse-graining of electrolyte solutions: Applications to aqueous NaCl and KCl J. Phys. Chem. B 2009, 113, 7785-7793
35. Hadley, K. R.; McCabe, C. A structurally relevant coarse-grained model for cholesterol Biophys. J. 2010, 99, 2896-2905
36. Hadley, K. R.; McCabe, C. A coarse-grained model for amorphous and crystalline fatty acids J. Chem. Phys. 2010, 132, 134505
37. Wang, Z. J.; Deserno, M. A Systematically Coarse-Grained Solvent-Free Model for Quantitative Phospholipid Bilayer Simulations J. Phys. Chem. B 2010, 114, 11207-11220
38. Mukherjee, B.; Delle Site, L.; Kremer, K.; Peter, C. Derivation of Coarse Grained Models for Multiscale Simulation of Liquid Crystalline Phase Transitions J. Phys. Chem. B 2012, 116, 8474-8484
39. Jochum, M.; Andrienko, D.; Kremer, K.; Peter, C. Structure-based coarse-graining in liquid slabs J. Chem. Phys. 2012, 137, 064102
40. Májek, P.; Elber, R. A Coarse-Grained Potential for Fold Recognition and Molecular Dynamics Simulations of Proteins Prot. Struct. Funct. Bioinfo. 2009, 76, 822-836
41. Bezkorovaynaya, O.; Lukyanov, A.; Kremer, K.; Peter, C. Multiscale simulation of small peptides: Consistent conformational sampling in atomistic and coarse-grained models J. Comput. Chem. 2012, 33, 937-949
42. Carmichael, S. P.; Shell, M. S. A new multiscale algorithm and its application to coarse-grained peptide models for self-assembly J. Phys. Chem. B 2012, 116, 8383-8393
43. Shell, M. S. The relative entropy is fundamental to multiscale and inverse thermodynamic problems J. Chem. Phys. 2008, 129, 144108
44. Chaimovich, A.; Shell, M. S. Coarse-graining errors and numerical optimization using a relative entropy framework J. Chem. Phys. 2011, 134, 094112
45. Rudzinski, J. F.; Noid, W. G. Coarse-graining entropy, forces, and structures J. Chem. Phys. 2011, 135, 214101
46. Kullback, S.; Leibler, R. A. On information and sufficiency Ann. Math. Stat. 1951, 22, 79-86
47. Murtola, T.; Karttunen, M.; Vattulainen, I. Systematic coarse graining from structure using internal states: Application to phospholipid/cholesterol bilayer J. Chem. Phys. 2009, 131, 055101
48. Izvekov, S.; Voth, G. A. A multiscale coarse-graining method for biomolecular systems J. Phys. Chem. B 2005, 109, 2469-2473
49. Izvekov, S.; Voth, G. A. Multiscale coarse graining of liquid-state systems J. Chem. Phys. 2005, 123, 134105
50. Ercolessi, F.; Adams, J. B. Interatomic potentials from first-principles calculations: The force-matching method Europhys. Lett. 1994, 26, 583
51. Noid, W. G.; Liu, P.; Wang, Y. T.; Chu, J.-W.; Ayton, G. S.; Izvekov, S.; Andersen, H. C.; Voth, G. A. The Multiscale Coarse-graining Method. II. Numerical implementation for molecular coarse-grained models J. Chem. Phys. 2008, 128, 244115
52. Rudzinski, J. F.; Noid, W. G. The role of many-body correlations in determining potentials for coarse-grained models of equilibrium structure J. Phys. Chem. B 2012, 116, 8621-8635
53. Hill, T. L. Statistical Mechanics: Principles and selected applications; Dover reprint, 1987.
54. Noid, W. G.; Chu, J.-W.; Ayton, G. S.; Voth, G. A. Multiscale Coarse-graining and Structural Correlations: Connections to Liquid State Theory J. Phys. Chem. B 2007, 111, 4116-4127
55. Mullinax, J. W.; Noid, W. G. A generalized Yvon-Born-Green theory for molecular systems Phys. Rev. Lett. 2009, 103, 198104
56. Mullinax, J. W.; Noid, W. G. A Generalized Yvon-Born-Green Theory for Determining Coarse-grained Interaction Potentials J. Phys. Chem. C 2010, 114, 5661-5674
57. Mullinax, J. W.; Noid, W. G. Reference state for the generalized Yvon-Born-Green theory: Application for a coarse-grained model of hydrophobic hydration J. Chem. Phys. 2010, 133, 124107
58. Ellis, C. R.; Rudzinski, J. F.; Noid, W. G. generalized-Yvon-Born-Green model for toluene Macromol. Theory Simul. 2011, 20, 478-495
59. Noid, W. G.; Ayton, G. S.; Izvekov, S.; Voth, G. A. In Coarse-graining of condensed phase and biomolecular systems; Voth, G. A., Ed.; CRC Press: Boca Raton, FL, USA, 2008; Chapter 3, pp 21-40.
60. Lu, L.; Voth, G. A. The Multiscale Coarse-Graining Method Adv. Chem. Phys. 2012, 149, 47-81
61. Ruhle, V.; Junghans, C.; Lukyanov, A.; Kremer, K.; Andrienko, D. Versatile Object-Oriented Toolkit for Coarse-Graining Applications J. Chem. Theor. Comput. 2009, 5, 3211-3223
62. Das, A.; Lu, L.; Andersen, H. C.; Voth, G. A. The multiscale coarse-graining method. X. Improved algorithms for constructing coarse-grained potentials for molecular systems J. Chem. Phys. 2012, 136, 194115
63. Mullinax, J. W.; Noid, W. G. Extended Ensemble approach for deriving transferable Coarse-grained potentials J. Chem. Phys. 2009, 131, 104110
64. Cho, H. M.; Chu, J. W. Inversion of radial distribution functions to pair forces by solving the Yvon-Born-Green equation iteratively J. Chem. Phys. 2009, 131, 134107
65. Lu, L.; Dama, J. F.; Voth, G. A. Fitting coarse-grained distribution functions through an iterative force-matching method J. Chem. Phys. 2013, 139, 121906
66. Tschop, W.; Kremer, K.; Hahn, O.; Batoulis, J.; Burger, T. Simulation of polymer melts. II. From coarse-grained models back to atomistic description Acta Polym. 1998, 49, 75-79
67. Arkhipov, A.; Freddolino, P.; Schulten, K. Stability and dynamics of virus capsids described by coarse-grained modeling Structure 2006, 129, 1767-1777
68. Harmandaris, V. A.; Reith, D.; Van der Vegt, N. F. A.; Kremer, K. Comparison between coarse-graining models for polymer systems: Two mapping schemes for polystyrene Macromol. Chem. Phys. 2007, 208, 2109-2120
69. Zhang, Z.; Voth, G. A. Coarse-Grained Representations of Large Biomolecular Complexes from Low-Resolution Structural Data J. Chem. Theor. Comput. 2010, 6, 2990-3002
70. Sinitskiy, A. V.; Saunders, M. G.; Voth, G. A. Optimal Number of Coarse-Grained Sites in Different Components of Large Biomolecular Complexes J. Phys. Chem. B 2012, 116, 8363-8374
71. Gohlke, H.; Thorpe, M. F. A natural coarse graining for simulating large biomolecular motion Biophys. J. 2006, 91, 2115-2120
72. Stepanova, M. Dynamics of essential collective motions in proteins: Theory Phys. Rev. E 2007, 76, 051918
73. Zhang, Z. Y.; Lu, L. Y.; Noid, W. G.; Krishna, V.; Pfaendtner, J.; Voth, G. A. A Systematic Methodology for Defining Coarse-Grained Sites in Large Biomolecules Biophys. J. 2008, 95, 5073-5083
74. Guttenberg, N.; Dama, J. F.; Saunders, M. G.; Voth, G. A.; Weare, J.; Dinner, A. R. Minimizing memory as an objective for coarse-graining J. Chem. Phys. 2013, 138, 094111
75. Lu, L. Y.; Izvekov, S.; Das, A.; Andersen, H. C.; Voth, G. A. Efficient, Regularized, and Scalable Algorithms for Multiscale Coarse-Graining J. Chem. Theor. Comput. 2010, 6, 954-965
76. Mullinax, J. W.; Noid, W. G. Recovering physical potentials from a model protein databank Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 19867-19872
77. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. Development and testing of the OPLS All-Atom force field on conformational energetics and properties of organic liquids J. Am. Chem. Soc. 1996, 118, 11225-11236
78. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation J. Chem. Theor. Comput. 2008, 4, 435-447
79. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. Molecular dynamics with coupling to an external bath J. Chem. Phys. 1984, 81, 3684-3690
80. Nose, S. A molecular dynamics method for simulations in the canonical ensemble Mol. Phys. 1984, 52, 255-268
81. Hoover, W. G. Canonical dynamics: Equilibrium phase-space distributions Phys. Rev. A 1985, 31, 1695-1697
82. Parrinello, M.; Rahman, A. Strain fluctuations and elastic constants J. Chem. Phys. 1982, 76, 2662-2666
83. Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: An N log(N) method for Ewald sums in large systems J. Chem. Phys. 1993, 99, 8345-8348
84. Allen, M. P.; Tildesley, D. P. Computer Simulation of Liquids; Oxford Press: New York, NY, USA, 1987.
85. Ramos-Estrada, M.; Iglesias-Silva, G.; Hall, K. Experimental measurements and prediction of liquid densities for n-alkane mixtures J. Chem. Thermodyn. 2006, 38, 337-347
86. Yaws, C. L. Thermophysical Properties of Chemicals and Hydrocarbons; William Andrew: Norwich, NY, USA, 2008.
87. Williams, T.; Kelley, C.; Gnuplot 4.4: an interactive plotting program. http://gnuplot.sourceforge.net/, 2010.
88. Chu, J.-W.; Voth, G. A. Coarse-Grained Modeling of the Actin Filament Derived from Atomistic-Scale Simulations Biophys. J. 2006, 90, 1572-1582
89. Anderson, E.; Bai, Z.; Bischof, C.; Blackford, S.; Demmel, J.; Dongarra, J.; Croz, J. D.; Greenbaum, A.; Hammarling, S.; McKenney, A.; Sorensen, D. LAPACK Users′ Guide; SIAM: Philadelphia, PA, USA, 1999.
90. Press, W. H.; Teukolsky, S. A.; Vetterling, W. T.; Flannery, B. P. Numerical Recipes in FORTRAN: The art of scientific computing; Cambridge University Press: New York, NY, USA, 1992.
91. Savelyev, A.; Papoian, G. A. Molecular renormalization group coarse-graining of polymer chains: Applications to double-stranded DNA Biophys. J. 2009, 96, 4044-4052
92. Evans, R. Comment on Reverse Monte Carlo Simulation Mol. Simul. 1990, 4, 409-411