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Communication: Simulated tempering with fast on-the-fly weight determination
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1.
1. A. Mitsutake, Y. Sugita, and Y. Okamoto, Biopolymers 60, 96 (2001).
http://dx.doi.org/10.1002/1097-0282(2001)60:2<96::AID-BIP1007>3.0.CO;2-F
2.
2. J. Kim, T. Keyes, and J. Straub, J. Chem. Phys. 132, 224107 (2010).
http://dx.doi.org/10.1063/1.3432176
3.
3. E. Rosta and G. Hummer, J. Chem. Phys. 132, 034102 (2010).
http://dx.doi.org/10.1063/1.3290767
4.
4. D. Sindhikara, D. Emerson, and A. Roitberg, J. Chem. Theory Comput. 6, 2804 (2010).
http://dx.doi.org/10.1021/ct100281c
5.
5. A. P. Lyubartsev, A. A. Martinovski, S. V. Shevkunov, and P. N. Vorontsov-Velyaminov, J. Chem. Phys. 96, 1776 (1992).
http://dx.doi.org/10.1063/1.462133
6.
6. E. Marinari and G. Parisi, Europhys. Lett. 19, 451 (1992).
http://dx.doi.org/10.1209/0295-5075/19/6/002
7.
7. C. J. Geyer, in Computing Science and Statistics: Proceedings of the 23rd Symposium on the Interface (Interface Foundation, Fairfax Station, 1991), pp. 156163.
8.
8. K. Hukushima and K. Nemoto, J. Phys. Soc. Jpn. 65, 1604 (1996).
http://dx.doi.org/10.1143/JPSJ.65.1604
9.
9. A. Mitsutake and Y. Okamoto, Chem. Phys. Lett. 332, 131 (2000).
http://dx.doi.org/10.1016/S0009-2614(00)01262-8
10.
10. C. Zhang and J. Ma, J. Chem. Phys. 129, 134112 (2008).
http://dx.doi.org/10.1063/1.2988339
11.
11. S. Rauscher, S. Rauscher, C. Neale, and R. Pomes, J. Chem. Theory Comput. 5, 2640 (2009).
http://dx.doi.org/10.1021/ct900302n
12.
12. A. Irbäck and F. Potthast, J. Chem. Phys. 103, 10298 (1995).
http://dx.doi.org/10.1063/1.469931
13.
13. U. Hansmann and Y. Okamoto, J. Comput. Chem. 18, 920 (1997).
http://dx.doi.org/10.1002/(SICI)1096-987X(199705)18:7<920::AID-JCC5>3.0.CO;2-T
14.
14. S. Park and V. Pande, Phys. Rev. E 76, 016703 (2007).
http://dx.doi.org/10.1103/PhysRevE.76.016703
15.
15. A. Mitsutake and Y. Okamoto, J. Chem. Phys. 121, 2491 (2004).
http://dx.doi.org/10.1063/1.1766015
16.
16. A. Mitsutake and Y. Okamoto, J. Chem. Phys. 130, 214105 (2009).
http://dx.doi.org/10.1063/1.3127783
17.
17. R. Denschlag, M. Lingenheil, P. Tavan, and G. Mathias, J. Chem. Theory Comput. 5, 2847 (2009).
http://dx.doi.org/10.1021/ct900274n
18.
18. R. Chelli, J. Chem. Theory Comput. 6, 1935 (2010).
http://dx.doi.org/10.1021/ct100105z
19.
19. Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 314, 141 (1999).
http://dx.doi.org/10.1016/S0009-2614(99)01123-9
20.
20. S. Park, Phys. Rev. E 77, 016709 (2008).
http://dx.doi.org/10.1103/PhysRevE.77.016709
21.
21. Y. Chebaro, S. Pasquali, and P. Derreumaux, J. Phys. Chem. B 116, 8741 (2012).
http://dx.doi.org/10.1021/jp301665f
22.
22. Y. Chebaro and P. Derreumaux, Proteins 75, 442 (2009).
http://dx.doi.org/10.1002/prot.22254
23.
23. Y. G. Spill, S. Pasquali, and P. Derreumaux, J. Chem. Theory. Comput. 7, 1502 (2011).
http://dx.doi.org/10.1021/ct100619p
24.
24. Y. Chebaro, X. Dong, R. Laghaei, P. Derreumaux, and N. Mousseau, J. Phys. Chem. B 113, 267 (2009).
http://dx.doi.org/10.1021/jp805309e
25.
25. P. H. Nguyen, M. S. Li, J. E. Straub, and D. Thirumalai, Proc. Natl. Acad. Sci. U.S.A. 104, 111 (2007).
http://dx.doi.org/10.1073/pnas.0607440104
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/content/aip/journal/jcp/138/6/10.1063/1.4792046
2013-02-12
2014-07-24

Abstract

We propose an efficient method to enhance sampling in computer simulations by combining the simulated tempering algorithm with a fast on-the-fly weight determination scheme. The weights are self-updated via a trapezoid rule during the simulated tempering simulation. With our proposed scheme, simulated tempering requires neither prior trial simulations nor complicated update schemes. The advantage of our method over replica exchange molecular dynamics has been demonstrated with the study of the folding of the 20-residue alanine peptide and the aggregation of a trimer formed by the Alzheimer's peptide fragment Aβ16−22.

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Scitation: Communication: Simulated tempering with fast on-the-fly weight determination
http://aip.metastore.ingenta.com/content/aip/journal/jcp/138/6/10.1063/1.4792046
10.1063/1.4792046
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