GSHMC: An efficient method for molecular simulation

Journal of Computational Physics

Volumn 227, Issue 10, 2008, Pages 4934-4954

  Akhmatskaya, Elena ^a   Reich, Sebastian ^b  

^a FUJITSU LABORATORIES LTD   (Japan)

^b UNIVERSITY OF POTSDAM   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR DYNAMICS; MONTE CARLO METHODS; STOCHASTIC SYSTEMS;

ACCEPTANCE CRITERIA; CANONICAL ENSEMBLE; CLASSICAL MOLECULAR DYNAMICS; DYNAMICS SIMULATION; ENERGY; HYBRID MONTE CARLO; HYBRID MONTE-CARLO METHODS; MOLECULAR SIMULATIONS; REJECTION RATES; RESAMPLING;

MOMENTUM;

EID: 41249100828     PISSN: 00219991     EISSN: 10902716     Source Type: Journal    
DOI: 10.1016/j.jcp.2008.01.023     Document Type: Article

References (37)

1. Duane S., Kennedy A.D., Pendleton B.J., and Roweth D. Phys. Lett. B 195 (1987) 216
2. Mehlig B., Heermann D.W., and Forrest B.M. Phys. Rev. B 45 (1992) 679
3. Izaguirre J.A., and Hampton S.S. J. Comput. Phys. 200 (2004) 581
4. Benettin G., and Giorgilli A. J. Stat. Phys. 74 (1994) 1117
5. Hairer E., and Lubich C. Numer. Math. 76 (1997) 441
6. Reich S. SIAM J. Numer. Anal. 36 (1999) 475
7. Leimkuhler B., and Reich S. Simulating Hamiltonian Dynamics (2005), Cambridge University Press, Cambridge
8. Hairer E., Lubich C., and Wanner G. Geometric Numerical Integration (2002), Springer-Verlag, Berlin, Heidelberg
9. Moore B., and Reich S. Numer. Math. 95 (2003) 625
10. Skeel R.D., and Hardy D.J. SIAM J. Sci. Comput. 23 (2001) 1172
11. C.R. Sweet, S.S. Hampton, J.A. Izaguirre, Tech. Rep. TR-2006-09, University of Notre Dame, 2006.
12. C.R. Sweet, S.S. Hampton, R.D. Skeel, J.A. Izaguirre, J. Chem. Phys., Submitted for publication.
13. E. Akhmatskaya, S. Reich, in: B. Leimkuhler et al. (Eds.), New Algorithms for Macromolecular Simulations, Lecture Notes in Computational Science and Engineering, vol. 49, Springer-Verlag, Berlin, 2006, pp. 145-158.
14. Horowitz A.M. Phys. Lett. B 268 (1991) 247
15. Kennedy A.D., and Pendleton B. Nucl. Phys. B 607 (2001) 456
16. Andersen H.C. J. Chem. Phys. 72 (1980) 2384
17. Feller S.E., Zhang Y., Pastor R.W., and Brooks B.R. J. Chem. Phys. 103 (1995) 4613
18. Allen M.P., and Tildesley D.J. Computer Simulation of Liquids (1987), Clarendon Press, Oxford
19. MacKay R. In: Broomhead D.S., and Iserles A. (Eds). The Dynamics of Numerics and the Numerics of Dynamics (1992), Clarendon Press, Oxford 137-193
20. Gupta S., Irbäck A., Karsch F., and Petersson B. Phys. Lett. B 242 (1990) 437
21. Burden R.L., and Faires J.D. Numerical Analysis. eighth ed. (2005), Brooks Cole
22. Ryckaert J.P., Ciccotti G., and Berendsen H.J.C. J. Comput. Phys. 23 (1977) 327
23. Faller R., and de Pablo J.J. J. Chem. Phys. 116 (2002) 55
24. Brünger A., Brooks III C.L., and Karplus M. Chem. Phys. Lett. 105 (1984)
25. Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., DiNola A., and Haak J.R. J. Chem. Phys. 81 (1984) 3684
26. Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., and Hermans J. In: Pullman B. (Ed). Intermolecular Forces (1981), D. Reidel Publishing Company, Dordrecht 331-342
27. Lindahl E., Hess B., and van der Spoel D. J. Mol. Model. 7 (2001) 306
28. Darden T., York D., and Pedersen L. J. Comput. Phys. 98 (1993) 10089
29. Essmann U., Perera L., Berkowitz M.L., Darden T.A., Lee H., and Pedersen L.G. J. Comput. Phys. 103 (1995) 8577
30. Humphrey W., Dalke A., and Schulten K. J. Mol. Graph. (1996) 33
31. Anderson W.F., Grütter M.G., Remington S.J., Weaver L.H., and Matthews B.W. J. Mol. Biol. 147 (1981) 523
32. Hardy L.W., and Poteete A.R. Biochemistry 30 (1991) 9457
33. Kuroki R., Weaver L.H., and Matthews B.W. Science 262 (1993) 2030
34. Kuroki R., Weaver L.H., and Matthews B.W. Nat. Struct. Biol. 2 (1995) 1007
35. Kuroki R., Weaver L.H., and Matthews B.W. Proc. Natl. Acad. Sci. 96 (1999) 8949
36. Neal R.M. Bayesian Learning for Neural Networks (1996), Springer-Verlag, New York
37. Liu J.S. Monte Carlo Strategies in Scientific Computing (2001), Springer-Verlag, New York