The multiscale coarse-graining method. V. Isothermal-isobaric ensemble

Journal of Chemical Physics

Volumn 132, Issue 16, 2010, Pages

  Das, Avisek ^a   Andersen, Hans C ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CANONICAL ENSEMBLE; COARSE GRAINING; COARSE-GRAINED; COARSE-GRAINING METHOD; CONFIGURATION SPACE; CONSTANT PRESSURES; CONSTANT VOLUMES; COULOMBIC FORCES; DETAILED MODELS; EFFECTIVE POTENTIALS; ENERGY FUNCTIONS; EWALD METHOD; MOLECULAR DYNAMICS SIMULATIONS; MULTISCALES; SHORT-RANGED INTERACTION; SIMPLE MODEL; VOLUME FLUCTUATIONS;

DISTRIBUTION FUNCTIONS; MOLECULAR DYNAMICS; POTENTIAL ENERGY FUNCTIONS;

COMPUTER SIMULATION;

EID: 77952397349     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3394862     Document Type: Article

References (68)

1. M. P. Allen and D. P. Tildesley, Computer Simulation of Liquids (Oxford University Press, Oxford, 1987).
2. M. Frenkel and B. Smit, Understanding Molecular Simulation: From Algorithms to Applications (Academic, New York, 2002).
3. S. O. Nielsen, C. F. Lopez, G. Srinivas, and M. L. Klein, J. Phys.: Condens. Matter JCOMEL 0953-8984 16, R481 (2004), and references therein. 10.1088/0953-8984/16/15/R03
4. T. Head-Gordon and S. Brown, Curr. Opin. Struct. Biol. COSBEF 0959-440X 13, 160 (2003), and references therein. 10.1016/S0959-440X(03)00030-7 (Pubitemid 36515143)
5. V. Tozzini, Curr. Opin. Struct. Biol. COSBEF 0959-440X 15, 144 (2005), and references therein. 10.1016/j.sbi.2005.02.005
6. I. Bahar and A. Rader, Curr. Opin. Struct. Biol. COSBEF 0959-440X 15, 586 (2005), and references therein. 10.1016/j.sbi.2005.08.007 (Pubitemid 41393491)
7. G. S. Ayton, W. G. Noid, and G. A. Voth, Curr. Opin. Struct. Biol. COSBEF 0959-440X 17, 192 (2007). 10.1016/j.sbi.2007.03.004 (Pubitemid 46584804)
8. M. Müller, K. Katsov, and M. Schick, Phys. Rep. PRPLCM 0370-1573 434, 113 (2006), and references therein. 10.1016/j.physrep.2006.08.003
9. 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, and V. Tries, Advances in Polymer Science (Springer-Verlag, Berlin/Heidelberg, 2000), Vol. 152, p. 41, and references therein.
10. Coarse-Graining of Condensed Phase and Biomolecular Systems, edited by, G. A. Voth, (CRC, Boca Raton, FL, 2009).
11. M. Levitt, J. Mol. Biol. JMOBAK 0022-2836 104, 59 (1976). 10.1016/0022-2836(76)90004-8
12. N. G and H. Abe, Biopolymers BIPMAA 0006-3525 20, 991 (1981). 10.1002/bip.1981.360200511
13. H. Abe and N. G, Biopolymers BIPMAA 0006-3525 20, 1013 (1981). 10.1002/bip.1981.360200512
14. S. Miyazawa and R. L. Jernigan, Macromolecules MAMOBX 0024-9297 18, 534 (1985). 10.1021/ma00145a039
15. A. P. Lyubartsev and A. Laaksonen, Phys. Rev. E. PLEEE8 1063-651X 52, 3730 (1995). 10.1103/PhysRevE.52.3730
16. J. C. Shelley, M. Y. Shelley, R. C. Reeder, S. Bandyopadhyay, and M. L. Klein, J. Phys. Chem. B JPCBFK 1089-5647 105, 4464 (2001). 10.1021/jp010238p (Pubitemid 35381588)
17. S. J. Marrink, A. H. de Vries, and A. E. Mark, J. Phys. Chem. B JPCBFK 1089-5647 108, 750 (2004). 10.1021/jp036508g
18. A. Liwo, S. Oldziej, C. Czaplewski, U. Kozlowska, and H. A. Scheraga, J. Phys. Chem. B JPCBFK 1089-5647 108, 9421 (2004). 10.1021/jp030844f
19. A. Liwo, C. Czaplewski, J. Pillardy, and H. A. Scheraga, J. Chem. Phys. JCPSA6 0021-9606 115, 2323 (2001). 10.1063/1.1383989 (Pubitemid 32742790)
20. I. G. Kevrekidis, C. W. Gear, and G. Hummer, AIChE J. AICEAC 0001-1541 50, 1346 (2004). 10.1002/aic.10106 (Pubitemid 38856761)
21. N. -V. Buchete, J. E. Straub, and D. Thirumalai, Protein Sci. PRCIEI 0961-8368 13, 862 (2004). 10.1110/ps.03488704 (Pubitemid 38429210)
22. D. Curcó, R. Nussinov, and C. Aleman, J. Phys. Chem. B JPCBFK 1089-5647 111, 14006 (2007). 10.1021/jp075386f
23. M. Lu and J. Ma, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 105, 15358 (2008). 10.1073/pnas.0806072105
24. M. A. Jonikas, R. J. Radmer, A. Laederach, R. Das, S. Pearlman, D. Herschlag, and R. B. Altman, RNA RNARFU 1355-8382 15, 189 (2009). 10.1261/rna.1270809
25. R. B. Pandey and B. L. Farmer, J. Chem. Phys. JCPSA6 0021-9606 130, 044906 (2009). 10.1063/1.3050106
26. T. Ha-Duong, N. Basdevant, and D. Borgis, Chem. Phys. Lett. CHPLBC 0009-2614 468, 79 (2009). 10.1016/j.cplett.2008.11.092
27. Z. Zhang and W. Wriggers, J. Phys. Chem. B JPCBFK 1089-5647 112, 14026 (2008). 10.1021/jp806291p
28. A. Y. Shih, A. Arkhipov, P. L. Freddolino, and K. Schulten, J. Phys. Chem. B JPCBFK 1089-5647 110, 3674 (2006). 10.1021/jp0550816
29. P. J. Bond, J. Holyoake, A. Ivetac, S. Khalid, and M. S. Sansom, J. Struct. Biol. JSBIEM 1047-8477 157, 593 (2007). 10.1016/j.jsb.2006.10.004
30. D. Reith, M. Pütz, and F. Müller-Plathe, J. Comput. Chem. JCCHDD 0192-8651 24, 1624 (2003). 10.1002/jcc.10307
31. L. Monticelli, S. K. Kandasamy, X. Periole, R. G. Larson, D. P. Tieleman, and S. -J. Marrink, J. Chem. Theory Comput. JCTCCE 1549-9618 4, 819 (2008). 10.1021/ct700324x
32. K. Moritsugu and J. C. Smith, Biophys. J. BIOJAU 0006-3495 95, 1639 (2008). 10.1529/biophysj.108.131714
33. C. F. Abrams, L. Delle Site, and K. Kremer, Phys. Rev. E. PLEEE8 1063-651X 67, 021807 (2003). 10.1103/PhysRevE.67.021807
34. R. E. Rudd and J. Q. Broughton, Phys. Rev. B PRBMDO 0163-1829 58, R5893 (1998). 10.1103/PhysRevB.58.R5893
35. R. L. C. Akkermans and W. J. Briels, J. Chem. Phys. JCPSA6 0021-9606 114, 1020 (2001). 10.1063/1.1330744 (Pubitemid 32138537)
36. H. Fukunaga, J. Takimoto, and M. Doi, J. Chem. Phys. JCPSA6 0021-9606 116, 8183 (2002). 10.1063/1.1469609 (Pubitemid 34555090)
37. S. O. Nielsen, C. F. Lopez, G. Srinivas, and M. L. Klein, J. Chem. Phys. JCPSA6 0021-9606 119, 7043 (2003). 10.1063/1.1607955
38. V. Molinero and W. A. Goddard, J. Phys. Chem. B JPCBFK 1089-5647 108, 1414 (2004). 10.1021/jp0354752
39. G. S. Ayton, H. L. Tepper, D. T. Mirijanian, and G. A. Voth, J. Chem. Phys. JCPSA6 0021-9606 120, 4074 (2004). 10.1063/1.1644092
40. S. D. Chao, J. D. Kress, and A. Redondo, J. Chem. Phys. JCPSA6 0021-9606 122, 234912 (2005). 10.1063/1.1938193 (Pubitemid 40925793)
41. V. Tozzini and J. A. McCammon, Chem. Phys. Lett. CHPLBC 0009-2614 413, 123 (2005). 10.1016/j.cplett.2005.07.075 (Pubitemid 41252378)
42. J. -W. Chu and G. A. Voth, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 102, 13111 (2005). 10.1073/pnas.0503732102 (Pubitemid 41324987)
43. P. A. Golubkov and P. Ren, J. Chem. Phys. JCPSA6 0021-9606 125, 064103 (2006). 10.1063/1.2244553
44. H. Gohlke and M. Thorpe, Biophys. J. BIOJAU 0006-3495 91, 2115 (2006). 10.1529/biophysj.106.083568 (Pubitemid 44352394)
45. D. A. Kondrashov, Q. Cui, and G. N. Phillips, Biophys. J. BIOJAU 0006-3495 91, 2760 (2006). 10.1529/biophysj.106.085894 (Pubitemid 44526467)
46. L. -J. Chen, H. -J. Qian, Z. -Y. Lu, Z. -S. Li, and C. -C. Sun, J. Phys. Chem. B JPCBFK 1089-5647 110, 24093 (2006). 10.1021/jp0644558 (Pubitemid 46065849)
47. S. Izvekov and G. A. Voth, J. Phys. Chem. B JPCBFK 1089-5647 109, 2469 (2005). 10.1021/jp044629q (Pubitemid 40304419)
48. S. Izvekov and G. A. Voth, J. Chem. Phys. JCPSA6 0021-9606 123, 134105 (2005). 10.1063/1.2038787 (Pubitemid 41434694)
49. Y. Wang, S. Izvekov, T. Yan, and G. A. Voth, J. Phys. Chem. B JPCBFK 1089-5647 110, 3564 (2006). 10.1021/jp0548220
50. S. Izvekov and G. A. Voth, J. Chem. Theory Comput. JCTCCE 1549-9618 2, 637 (2006). 10.1021/ct050300c
51. J. Zhou, I. F. Thorpe, S. Izvekov, and G. A. Voth, Biophys. J. BIOJAU 0006-3495 92, 4289 (2007). 10.1529/biophysj.106.094425 (Pubitemid 46910544)
52. I. F. Thorpe, J. Zhou, and G. A. Voth, J. Phys. Chem. B JPCBFK 1089-5647 112, 13079 (2008). 10.1021/jp8015968
53. S. Izvekov, A. Violi, and G. A. Voth, J. Phys. Chem. B JPCBFK 1089-5647 109, 17019 (2005). 10.1021/jp0530496 (Pubitemid 41361374)
54. Q. Shi, S. Izvekov, and G. A. Voth, J. Phys. Chem. B JPCBFK 1089-5647 110, 15045 (2006). 10.1021/jp062700h (Pubitemid 44318467)
55. W. G. Noid, J. -W. Chu, G. S. Ayton, V. Krishna, S. Izvekov, G. A. Voth, A. Das, and H. C. Andersen, J. Chem. Phys. JCPSA6 0021-9606 128, 244114 (2008). 10.1063/1.2938860
56. W. G. Noid, P. Liu, Y. Wang, J. -W. Chu, G. S. Ayton, S. Izvekov, H. C. Andersen, and G. A. Voth, J. Chem. Phys. JCPSA6 0021-9606 128, 244115 (2008). 10.1063/1.2938857
57. L. Lu and G. A. Voth, J. Phys. Chem. B JPCBFK 1089-5647 113, 1501 (2009). 10.1021/jp809604k
58. A. Das and H. C. Andersen, J. Chem. Phys. JCPSA6 0021-9606 131, 034102 (2009). 10.1063/1.3173812
59. D. A. McQuarrie, Statistical Mechanics (Viva Books, New Delhi, 2003).
60. I. R. McDonald, Mol. Phys. MOPHAM 0026-8976 23, 41 (1972). 10.1080/00268977200100031
61. H. C. Andersen, J. Chem. Phys. JCPSA6 0021-9606 72, 2384 (1980). 10.1063/1.439486
62. If we had attempted to carry out this derivation using unscaled coordinates, we would not be able to get simple results like Eqs. for the following reason. The mapping operator for unscaled coordinates in a periodic system with fluctuating volume depends explicitly on volume in a complicated way and, consequently, gives rise to nonzero partial derivatives with respect to volume. This would have led to much more complicated results and might have made the calculations intractable. This problem is avoided by performing the calculation using the scaled coordinates, where the position mapping operator does not have any explicit volume dependence, leading to much simpler expressions.
63. Here we are concerned only with the case of homogeneous isotropic fluid systems. For other systems, different considerations will, of course, apply.
64. W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery, Numerical Recipes in C: The Art of Scientific Computing (Cambridge University Press, Cambridge, 1992).
65. v (Q) contribution to the pressure, but the method for doing so could be derived from the current work. Attempts to calculate the virial pressure of a CG system without taking this term into account cannot generally get the correct answer. For a simple example, see Appendix for a discussion of an ideal gas mixture.
66. J. B. Sturgeon and B. B. Laird, J. Chem. Phys. JCPSA6 0021-9606 112, 3474 (2000). 10.1063/1.480502
67. J. M. Sanz-Serna and M. P. Calvo, Numerical Hamiltonian Problems (Chapman and Hall, London, 1994).
68. E. Hairer, C. Lubich, and G. Wanner, Geometric Numerical Integration: Structure-Preserving Algorithms for Ordinary Differential Equations (Springer, Berlin, 2006).