Free-energy calculation via mean-force dynamics using a logarithmic energy landscape

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 85, Issue 6, 2012, Pages

  Morishita, Tetsuya ^a,b   Itoh, Satoru G ^c,d   Okumura, Hisashi ^c,d   Mikami, Masuhiro ^a,b,e  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c INSTITUTE FOR MOLECULAR SCIENCE   (Japan)

^d GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

^e UNIVERSITY OF TSUKUBA   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CONSERVED QUANTITY; CONVENTIONAL METHODS; DIPEPTIDE; EFFICIENT SAMPLING; ENERGY LANDSCAPE; FREE-ENERGY CALCULATIONS; FREE-ENERGY LANDSCAPE; METADYNAMICS; ON-THE-FLY; POTENTIAL OF MEAN FORCE;

AMINO ACIDS; DYNAMICS;

FREE ENERGY;

EID: 84862192623     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.85.066702     Document Type: Article

References (18)

1. D. J. Wales, Energy Landscapes (Cambridge University Press, Cambridge, 2003).
2. D. Frenkel and B. Smit, Understanding Molecular Simulation: From Algorithms to Applications (Academic Press, San Diego, 2002).
3. G. M. Torrie and J. P. Valleau, J. Comput. Phys. 0021-9991 10.1016/0021-9991(77)90121-8 23, 187 (1977).
4. L. Rosso, P. Mináry, Z. Zhu, and M. E. Tuckerman, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1448491 116, 4389 (2002). (Pubitemid 34405135)
5. A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. USA PNASA6 0027-8424 10.1073/pnas.202427399 99, 12562 (2002);
6. A. Laio and F. L. Gervasio, Rep. Prog. Phys. 0034-4885 10.1088/0034-4885/71/12/126601 71, 126601 (2008).
7. J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B JPCBFK 1520-6106 10.1021/jp805039u 112, 15742 (2008).
8. L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/j.cplett.2006.05.062 426, 168 (2006).
9. J. B. Abrams, L. Rosso, and M. E. Tuckerman, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2232082 125, 074115 (2006). (Pubitemid 44267416)
10. C. F. Abrams and E. Vanden-Eijnden, Proc. Natl. Acad. Sci. USA PNASA6 0027-8424 10.1073/pnas.0914540107 107, 4961 (2010).
11. S. Nosé, Prog. Theor. Phys. Suppl. PTPSAL 0375-9687 10.1143/PTPS.103.1 103, 1 (1991).
12. R. Car and M. Parrinello, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.55.2471 55, 2471 (1985).
13. M. E. Tuckerman, B. J. Berne, and G. J. Martyna, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.463137 97, 1990 (1992).
14. T. Morishita, Mol. Phys. MOPHAM 0026-8976 10.1080/00268971003689923 108, 1337 (2010).
15. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.61.2635 61, 2635 (1988);
16. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.63.1658.2 63, 1658 (1989).
17. A. D. MacKerell Jr., D. Bashford, M. Bellott, R. L. Dunbrack Jr., J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiórkiewicz-Kuczera, D. Yin, and M. Karplus, J. Phys. Chem. B JPCBFK 1520-6106 10.1021/jp973084f 102, 3586 (1998).
18. G. J. Martyna, M. L. Klein, and M. E. Tuckerman, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.463940 97, 2635 (1992).