Time reversible molecular dynamics algorithms with holonomic bond constraints in the NPH and NPT ensembles using molecular scaling

Journal of Chemical Physics

Volumn 132, Issue 15, 2010, Pages

  Ingebrigtsen, Trond ^a,b   Heilmann, Ole J ^b   Toxvaerd, Søren ^b   Dyre, Jeppe C ^b  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b ROSKILDE UNIVERSITY   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

FLUCTUATION FORMULAS; HEAT CAPACITIES; HIGH-PRESSURE STATE; ISOBARIC HEAT CAPACITY; MACHINE PRECISION; MODIFIED EQUATION; MOLECULAR DYNAMICS ALGORITHMS; ORTHO-TERPHENYL; PHASE SPACES; TARGET TEMPERATURE; TIME REVERSIBLE;

ALGORITHMS; MECHANICS; MOLECULAR DYNAMICS; PHASE SPACE METHODS; SPECIFIC HEAT; UNCERTAINTY ANALYSIS;

EQUATIONS OF MOTION;

EID: 77951687003     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3363609     Document Type: Article

References (44)

1. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Oxford University Press, Oxford, 2003).
2. D. Frenkel and B. Smit, Understanding Molecular Simulation (Academic, New York, 2002).
3. M. Tuckerman, B. J. Berne, and G. J. Martyna, J. Chem. Phys. JCPSA6 0021-9606 97, 1990 (1992). 10.1063/1.463137
4. J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comput. Phys. JCTPAH 0021-9991 23, 327 (1977). 10.1016/0021-9991(77)90098-5
5. G. Ciccotti, M. Ferrario, and J. P. Ryckaert, Mol. Phys. MOPHAM 0026-8976 47, 1253 (1982). 10.1080/00268978200100942
6. H. C. Andersen, J. Comput. Phys. JCTPAH 0021-9991 52, 24 (1983). 10.1016/0021-9991(83)90014-1
7. J. P. Ryckaert and G. Ciccotti, J. Chem. Phys. JCPSA6 0021-9606 78, 7368 (1983). 10.1063/1.444728
8. R. Edberg, D. J. Evans, and G. P. Morriss, J. Chem. Phys. JCPSA6 0021-9606 84, 6933 (1986). 10.1063/1.450613
9. S. G. Lambrakos, J. P. Boris, E. S. Oran, I. Chandrasekhar, and M. Nagumo, J. Comput. Phys. JCTPAH 0021-9991 85, 473 (1989). 10.1016/0021-9991(89) 90160-5
10. B. J. Leimkuhler and R. D. Skeel, J. Comput. Phys. JCTPAH 0021-9991 112, 117 (1994). 10.1006/jcph.1994.1085 (Pubitemid 124013417)
11. B. Hess, H. Bekker, H. J. C. Berendsen, and J. G. E. M. Fraaije, J. Comput. Chem. JCCHDD 0192-8651 18, 1463 (1997). 10.1002/(SICI)1096-987X(199709) 18:12<1463::AID-JCC4>3.0.CO;2-H
12. V. Kräutler, W. F. van Gunsteren, and P. H. Hünenberger, J. Comput. Chem. JCCHDD 0192-8651 22, 501 (2001). 10.1002/1096-987X(20010415)22: 5<501::AID-JCC1021>3.0.CO;2-V
13. A. G. Bailey, C. P. Lowe, and A. P. Sutton, J. Comput. Phys. JCTPAH 0021-9991 227, 8949 (2008). 10.1016/j.jcp.2008.07.002
14. S. Toxvaerd, O. J. Heilmann, T. Ingebrigtsen, T. B. Schrøder, and J. C. Dyre, J. Chem. Phys. JCPSA6 0021-9606 131, 064102 (2009). 10.1063/1.3194785
15. A. G. Bailey and C. P. Lowe, J. Comput. Chem. JCCHDD 0192-8651 30, 2485 (2009). 10.1002/jcc.21237
16. P. Eastman and V. S. Pande, J. Chem. Theory Comput. JCTCCE 1549-9618 6, 434 (2010). 10.1021/ct900463w
17. H. C. Andersen, J. Chem. Phys. JCPSA6 0021-9606 72, 2384 (1980). 10.1063/1.439486
18. S. Noś, J. Chem. Phys. JCPSA6 0021-9606 81, 511 (1984). 10.1063/1.447334
19. W. G. Hoover, Phys. Rev. A PLRAAN 1050-2947 31, 1695 (1985). 10.1103/PhysRevA.31.1695
20. G. J. Martyna, D. J. Tobias, and M. L. Klein, J. Chem. Phys. JCPSA6 0021-9606 101, 4177 (1994). 10.1063/1.467468
21. S. Melchionna and G. Ciccotti, J. Chem. Phys. JCPSA6 0021-9606 106, 195 (1997). 10.1063/1.473041
22. A. Sergi, M. Ferrario, and D. Costa, Mol. Phys. MOPHAM 0026-8976 97, 825 (1999). 10.1080/00268979909482883
23. G. R. Kneller and T. Mülders, Phys. Rev. E PLEEE8 1063-651X 54, 6825 (1996). 10.1103/PhysRevE.54.6825
24. T. Mülders, S. Toxvaerd, and G. R. Kneller, Phys. Rev. E PLEEE8 1063-651X 58, 6766 (1998). 10.1103/PhysRevE.58.6766
25. G. Ciccotti, G. J. Martyna, S. Melchionna, and M. E. Tuckerman, J. Phys. Chem. B JPCBFK 1089-5647 105, 6710 (2001). 10.1021/jp010601s (Pubitemid 35339042)
26. G. Kalibaeva, M. Ferrario, and G. Ciccotti, Mol. Phys. MOPHAM 0026-8976 101, 765 (2003). 10.1080/0026897021000044025
27. H. A. Stern, J. Comput. Chem. JCCHDD 0192-8651 25, 749 (2004). 10.1002/jcc.20001
28. L. J. Lewis and G. Wahnström, Phys. Rev. E PLEEE8 1063-651X 50, 3865 (1994). 10.1103/PhysRevE.50.3865
29. H. Goldstein, C. Poole, and J. Safko, Classical Mechanics (Addison-Wesley, Reading, MA, 2002).
30. A. Sergi, Phys. Rev. E PLEEE8 1063-651X 69, 021109 (2004). 10.1103/PhysRevE.69.021109
31. A. Sergi and M. Ferrario, Phys. Rev. E PLEEE8 1063-651X 64, 056125 (2001). 10.1103/PhysRevE.64.056125
32. K. Cho, J. D. Joannopoulos, and L. Kleinman, Phys. Rev. E PLEEE8 1063-651X 47, 3145 (1993). 10.1103/PhysRevE.47.3145
33. M. E. Tuckerman, Y. Liu, G. Ciccotti, and G. J. Martyna, J. Chem. Phys. JCPSA6 0021-9606 115, 1678 (2001). 10.1063/1.1378321 (Pubitemid 32715517)
34. V. Marry and G. Ciccotti, J. Comput. Phys. JCTPAH 0021-9991 222, 428 (2007). 10.1016/j.jcp.2006.07.033
35. J. M. Haile and H. W. Graben, J. Chem. Phys. JCPSA6 0021-9606 73, 2412 (1980). 10.1063/1.440391
36. H. Ishida and A. Kidera, J. Chem. Phys. JCPSA6 0021-9606 109, 3276 (1998). 10.1063/1.476919 (Pubitemid 128678228)
37. S. Toxvaerd, Mol. Phys. MOPHAM 0026-8976 72, 159 (1991). 10.1080/00268979100100101
38. S. Jang and G. A. Voth, J. Chem. Phys. JCPSA6 0021-9606 107, 9514 (1997). 10.1063/1.475247
39. F. Legoll and R. Monneau, J. Chem. Phys. JCPSA6 0021-9606 117, 10452 (2002). 10.1063/1.1519842
40. T. Yamamoto, J. Chem. Phys. JCPSA6 0021-9606 124, 217101 (2006). 10.1063/1.2202355 (Pubitemid 43877843)
41. S. Toxvaerd, Phys. Rev. E PLEEE8 1063-651X 47, 343 (1993). 10.1103/PhysRevE.47.343
42. G. S. Ezra, J. Chem. Phys. JCPSA6 0021-9606 125, 034104 (2006). 10.1063/1.2215608 (Pubitemid 44107128)
43. B.
44. J. R. Ray, H. W. Graben, and J. M. Haile, Nuovo Cimento B NCIBAW 0369-3554 64, 191 (1981). 10.1007/BF02903282