메뉴 건너뛰기




Volumn 134, Issue 5, 2011, Pages

Escorted free energy simulations

Author keywords

[No Author keywords available]

Indexed keywords

ENERGY ESTIMATES; EXTERNAL WORK; FLUCTUATION THEOREMS; FREE ENERGY PERTURBATION; FREE ENERGY SIMULATIONS; FREE-ENERGY DIFFERENCE; MODEL SYSTEM; MONTE CARLO SIMULATION; NON EQUILIBRIUM;

EID: 79951538475     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3544679     Document Type: Article
Times cited : (32)

References (39)
  • 3
    • 4243754128 scopus 로고    scopus 로고
    • 690. 10.1103/PhysRevLett.78.2690
    • C. Jarzynski, Phys. Rev. Lett. 78, 2 690 (1997). 10.1103/PhysRevLett.78. 2690
    • (1997) Phys. Rev. Lett. , vol.78 , pp. 2
    • Jarzynski, C.1
  • 4
    • 0001965777 scopus 로고    scopus 로고
    • 018. 10.1103/PhysRevE.56.R5
    • C. Jarzynski, Phys. Rev. E 56, 5 018 (1997). 10.1103/PhysRevE.56.R5
    • (1997) Phys. Rev. E. , vol.56 , pp. 5
    • Jarzynski, C.1
  • 5
    • 34547791286 scopus 로고    scopus 로고
    • On the sampling requirements for exponential-work free-energy calculations
    • DOI 10.1080/00268970601074421, PII 769949532, Seventh Liblice Conference on the Statistical Mechanics of Liquids
    • D. A. Kofke, Mol. Phys. 104, 3701 (2006), and references therein. 10.1080/00268970601074421 (Pubitemid 47226640)
    • (2006) Molecular Physics , vol.104 , Issue.22-24 , pp. 3701-3708
    • Kofke, D.A.1
  • 6
    • 33645666178 scopus 로고    scopus 로고
    • 10.1103/PhysRevE.73.046105
    • C. Jarzynski, Phys. Rev. E 73, 046105 (2006). 10.1103/PhysRevE.73.046105
    • (2006) Phys. Rev. E. , vol.73 , pp. 046105
    • Jarzynski, C.1
  • 9
    • 0000886606 scopus 로고
    • 10.1021/j100165a045
    • R. Wood, J. Phys. Chem. 95, 4838 (1991). 10.1021/j100165a045
    • (1991) J. Phys. Chem. , vol.95 , pp. 4838
    • Wood, R.1
  • 10
    • 6944235692 scopus 로고
    • 10.1021/j100176a002
    • J. Hermans, J. Phys. Chem. 95, 9029 (1991). 10.1021/j100176a002
    • (1991) J. Phys. Chem. , vol.95 , pp. 9029
    • Hermans, J.1
  • 11
    • 79051471419 scopus 로고    scopus 로고
    • 10.1209/0295-5075/87/60005
    • S. Vaikuntanathan and C. Jarzynski, EPL 87, 60005 (2009). 10.1209/0295-5075/87/60005
    • (2009) EPL , vol.87 , pp. 60005
    • Vaikuntanathan, S.1    Jarzynski, C.2
  • 12
    • 43949083060 scopus 로고    scopus 로고
    • Escorted free energy simulations: Improving convergence by reducing dissipation
    • DOI 10.1103/PhysRevLett.100.190601
    • S. Vaikuntanathan and C. Jarzysnki, Phys. Rev. Lett. 100, 190601 (2008). 10.1103/PhysRevLett.100.190601 (Pubitemid 351705647)
    • (2008) Physical Review Letters , vol.100 , Issue.19 , pp. 190601
    • Vaikuntanathan, S.1    Jarzynski, C.2
  • 14
    • 59349102990 scopus 로고    scopus 로고
    • 10.1103/PhysRevE.79.011113
    • A. M. Hahn and H. Then, Phys. Rev. E 79, 011113 (2009). 10.1103/PhysRevE.79.011113
    • (2009) Phys. Rev. E. , vol.79 , pp. 011113
    • Hahn, A.M.1    Then, H.2
  • 15
    • 0034322921 scopus 로고    scopus 로고
    • Efficient free energy calculations by variationally optimized metric scaling: Concepts and applications to the volume dependence of cluster free energies and to solid-solid phase transitions
    • DOI 10.1063/1.1313537
    • M. A. Miller and W. P. Reinhardt, J. Chem. Phys. 113, 7035 (2000). 10.1063/1.1313537 (Pubitemid 32021200)
    • (2000) Journal of Chemical Physics , vol.113 , Issue.17 , pp. 7035-7046
    • Miller, M.A.1    Reinhardt, W.P.2
  • 16
    • 0000186593 scopus 로고    scopus 로고
    • 10.1103/PhysRevE.61.2361
    • G. Crooks, Phys. Rev. E 61, 2361 (2000). 10.1103/PhysRevE.61.2361
    • (2000) Phys. Rev. E. , vol.61 , pp. 2361
    • Crooks, G.1
  • 17
    • 0032023968 scopus 로고    scopus 로고
    • 10.1023/A:1023208217925
    • G. E. Crooks, J. Stat. Phys. 90, 1481 (1998). 10.1023/A:1023208217925
    • (1998) J. Stat. Phys. , vol.90 , pp. 1481
    • Crooks, G.E.1
  • 18
    • 0000765761 scopus 로고    scopus 로고
    • 10.1103/PhysRevE.60.2721
    • G. E. Crooks, Phys. Rev. E 60, 2721 (1999). 10.1103/PhysRevE.60.2721
    • (1999) Phys. Rev. E. , vol.60 , pp. 2721
    • Crooks, G.E.1
  • 19
    • 5244304444 scopus 로고
    • 10.1016/0021-9991(76)90078-4
    • C. H. Bennett, J. Comput. Phys. 22, 245 (1976). 10.1016/0021-9991(76) 90078-4
    • (1976) J. Comput. Phys. , vol.22 , pp. 245
    • Bennett, C.H.1
  • 21
    • 79951541680 scopus 로고    scopus 로고
    • As is usually the case with Monte Carlo simulations, we do not include momenta in the microstate
    • As is usually the case with Monte Carlo simulations, we do not include momenta in the microstate.
  • 25
  • 26
    • 50849121108 scopus 로고    scopus 로고
    • 10.1103/PhysRevLett.101.090602
    • E. H. Feng and G. E. Crooks, Phys. Rev. Lett. 101, 090602 (2008). 10.1103/PhysRevLett.101.090602
    • (2008) Phys. Rev. Lett. , vol.101 , pp. 090602
    • Feng, E.H.1    Crooks, G.E.2
  • 28
    • 77951099546 scopus 로고    scopus 로고
    • 10.1103/PhysRevE.81.041117
    • A. M. Hahn and H. Then, Phys. Rev. E 81, 041117 (2010). 10.1103/PhysRevE.81.041117
    • (2010) Phys. Rev. E. , vol.81 , pp. 041117
    • Hahn, A.M.1    Then, H.2
  • 29
    • 79951534984 scopus 로고    scopus 로고
    • 106 is reliable if C ∼ 0.001
    • 106 is reliable if C ∼ 0.001.
  • 30
    • 79951520825 scopus 로고    scopus 로고
    • i, including the eight corners, onto the region R-{i+1}$\end{document}]] rRi+1. However, due to the geometric mismatch between the spherical inner surface and cubic outer surface of these regions, such a mapping is not represented by a simple formula such as Eq., and would need to be constructed numerically
    • i, including the eight corners, onto the region R-{i+1}$\end{document}]] rRi+1. However, due to the geometric mismatch between the spherical inner surface and cubic outer surface of these regions, such a mapping is not represented by a simple formula such as Eq., and would need to be constructed numerically.
  • 33
    • 79951520340 scopus 로고    scopus 로고
    • Of course, even after dividing the problem into stages, one can apply escorting by separately treating each stage as a switching simulation with one step, N 1, and using the mappings given by Eq.. We found that this further reduces the error bars by nearly a factor of six
    • Of course, even after dividing the problem into stages, one can apply escorting by separately treating each stage as a switching simulation with one step, N 1, and using the mappings given by Eq.. We found that this further reduces the error bars by nearly a factor of six.
  • 36
    • 34548080273 scopus 로고    scopus 로고
    • Rosenbluth-sampled nonequilibrium work method for calculation of free energies in molecular simulation
    • DOI 10.1063/1.1906209, 204104
    • D. Wu and D. A. Kofke, J. Chem. Phys. 122, 204104 (2005). 10.1063/1.1906209 (Pubitemid 40858466)
    • (2005) Journal of Chemical Physics , vol.122 , Issue.20 , pp. 1-13
    • Wu, D.1    Kofke, D.A.2
  • 37
    • 0037396901 scopus 로고    scopus 로고
    • 10.1063/1.1557413
    • S. X. Sun, J. Chem. Phys. 118, 5759 (2003). 10.1063/1.1557413
    • (2003) J. Chem. Phys. , vol.118 , pp. 5759
    • Sun, S.X.1
  • 38
  • 39
    • 0000003059 scopus 로고    scopus 로고
    • 10.1002/(SICI)1096-987X(199705)18:902::AID-JCC43.0CO;2-V
    • R. J. Radmer and P. Kollman, J. Comp. Chem. 18, 902 10.1002/(SICI)1096- 987X(199705)18:902::AID-JCC43.0CO;2-V (1997).
    • (1997) J. Comp. Chem. , vol.18 , pp. 902
    • Radmer, R.J.1    Kollman, P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.