The Flexible Rare Event Sampling Harness System (FRESHS)

Computer Physics Communications

Volumn 185, Issue 7, 2014, Pages 1875-1885

  Kratzer, Kai ^a   Berryman, Joshua T ^b   Taudt, Aaron ^a   Zeman, Johannes ^a   Arnold, Axel ^a  

^a UNIVERSITY OF STUTTGART   (Germany)

^b UNIVERSITY OF LUXEMBOURG   (Luxembourg)

Author keywords

Chemical physics; ESPResSo; Forward Flux Sampling (FFS); GROMACS; HPC; LAMMPS; Rare event sampling; Stochastic Process Rare Event Sampling (SPRES)

Indexed keywords

COMPUTER SIMULATION; HETEROGENEOUS NETWORKS; OPEN SOURCE SOFTWARE; RANDOM PROCESSES;

CHEMICAL PHYSICS; ESPRESSO; FORWARD FLUX SAMPLING (FFS); GROMACS; HPC; LAMMPS;

OPTIMAL SYSTEMS;

EID: 84901591847     PISSN: 00104655     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cpc.2014.03.013     Document Type: Article

References (54)

1. T. Schilling, H. Schöpe, M. Oettel, G. Opletal, and I. Snook Phys. Rev. Lett. 105 2010 025701
2. C. Dekker Nat. Nanotech. 2 2007 209
3. R.J. Allen, P.B. Warren, and P.R. ten Wolde Phys. Rev. Lett. 94 2005 018104
4. R.J. Allen, D. Frenkel, and P.R. ten Wolde J. Chem. Phys. 124 2006 024102
5. R.J. Allen, D. Frenkel, and P.R. ten Wolde J. Chem. Phys. 124 2006 194111
6. R.J. Allen, C. Valeriani, and P.R. ten Wolde J. Phys.: Condens. Matter 21 2009 463102
7. C. Valeriani, R.J. Allen, M.J. Morelli, D. Frenkel, and P.R. ten Wolde J. Chem. Phys. 127 2007 114109
8. J.T. Berryman, and T. Schilling J. Chem. Phys. 133 2010 244101
9. M. Villén-Altamirano, and J. Villén-Altamirano Proceedings of the 26th Conference on Winter Simulation, WSC '94 1994 Society for Computer Simulation International San Diego, CA, USA 282 289
10. F. Cérou, A. Guyader, Rapport de recherche RR-5710, INRIA, 2005.
11. H. Kahn, and T. Harris National Bureau of Standards Applied Mathematics Series vol. 12 1951 27
12. Y. Dorozhko, K. Kratzer, Y. Yudin, A. Arnold, C. Glass, and M. Resch B.H.V. Topping, P. Iványi, Proceedings of the Fourteenth International Conference on Civil, Structural and Environmental Engineering Computing 2013 Civil-Comp Press Stirlingshire, UK Paper 207
13. C. Dellago, P.G. Bolhuis, F.S. Csajka, and D. Chandler J. Chem. Phys. 108 1998 1964
14. C. Dellago, P.G. Bolhuis, and P.L. Geissler Adv. Chem. Phys. 123 2002 1
15. P.G. Bolhuis, D. Chandler, C. Dellago, and P.L. Geissler Annu. Rev. Phys. Chem. 53 2002 291
16. E.E. Borrero, and F.A. Escobedo J. Phys. Chem. B 113 2009 6434
17. E.E. Borrero, and F.A. Escobedo J. Chem. Phys. 127 2007 164101
18. T.S. van Erp, D. Moroni, and P.G. Bolhuis J. Chem. Phys. 118 2003 7762
19. T.S. van Erp, and P.G. Bolhuis J. Comput. Phys. 205 2005 157
20. T.S. van Erp Comp. Phys. Commun. 179 2008 34
21. G.M. Torrie, and J.P. Valleau Chem. Phys. Lett. 28 1974 578
22. D. Frenkel, and B. Smit Understanding Molecular Simulation. From Algorithms to Applications second ed. 2002 Academic Press Boston
23. D. Chandler J. Chem. Phys. 68 1978 2959
24. C.H. Bennett R. Christofferson, Algorithms for Chemical Computations ACS Symposium, Series No. 46 1977 American Chemical Society Washington, D.C.
25. G. Henkelman, B.P. Uberuaga, and H. Jonsson J. Chem. Phys. 113 2000 9901
26. G. Henkelman, and H. Jonsson J. Chem. Phys. 113 2000 9978
27. A.K. Faradjian, and R. Elber J. Chem. Phys. 120 2004 10880
28. A.M.A. West, R. Elber, and D. Shalloway J. Chem. Phys. 126 2007 145104
29. E. Vanden-Eijnden, M. Venturoli, G. Ciccotti, and R. Elber J. Chem. Phys. 129 2008 174102
30. G.A. Huber, and S. Kim Biophys. J. 70 1996 97
31. W. E, W. Ren, and E. Vanden-Eijnden Phys. Rev. B 66 2002 052301
32. W. E, W. Ren, and E. Vanden-Eijnden J. Phys. Chem. B 109 2005 6688
33. A. Dickson, and A.R. Dinner Annu. Rev. Phys. Chem. 61 2010 441
34. A. Warmflash, P. Bhimalapuram, and A. Dinner J. Chem. Phys. 127 2007 154112
35. F.A. Escobedo, E.E. Borrero, and J.C. Araque J. Phys.: Condens. Matter 21 33 2009 333101
36. H. Berendsen, D. van der Spoel, and R. van Drunen Comput. Phys. Commun. 91 1995 43
37. S. Plimpton J. Comput. Phys. 117 1995 1
38. B.A.M. Hans-Jörg Limbach, Axel Arnold, and C. Holm Comput. Phys. Commun. 174 9 2006 704
39. L. Filion, M. Hermes, R. Ni, and M. Dijkstra J. Chem. Phys. 133 2010 244115
40. C. Valeriani, E. Sanz, and D. Frenkel J. Chem. Phys. 122 2005 194501
41. C. Velez-Vega, E.E. Borrero, and F.A. Escobedo J. Chem. Phys. 130 2009 225101
42. E.E. Borrero, and F.A. Escobedo J. Chem. Phys. 125 2006 164904
43. N.B. Becker, R.J. Allen, and P.R. ten Wolde J. Chem. Phys. 136 2012 174118
44. M. Bonomi, D. Branduardi, G. Bussi, C. Camilloni, D. Provasi, P. Raiteri, D. Donadio, F. Marinelli, F. Pietrucci, and R.A. Broglia et al. Comput. Phys. Commun. 180 2009 1961
45. M.U. Bohner, J. Zeman, J. Smiatek, A. Arnold, and J. Kästner J. Chem. Phys. 140 2014
46. K. Kratzer, A. Arnold, and R.J. Allen J. Chem. Phys. 138 2013 164112
47. E.E. Borrero, and F.A. Escobedo J. Chem. Phys. 129 2008 024115
48. M.W. Larsen, U.T. Bornscheuer, and K. Hult Protein Expr. Purif. 62 2008 90
49. J. Uppenberg, M.T. Hansen, S. Patkar, and T. Jones Structure 2 1994 293
50. E. Krissinel, and K. Henrick J. Mol. Biol. 2007
51. P.R. ten Wolde, and D. Frenkel J. Chem. Phys. 109 1998 9901
52. A. Kolb, and B. Dünweg J. Chem. Phys. 111 1999 4453
53. P.R. ten Wolde, M.J. Ruiz-Montero, and D. Frenkel J. Chem. Phys. 110 1999 1591
54. J.D. Weeks, D. Chandler, and H.C. Andersen J. Chem. Phys. 54 1971 5237