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Volumn 120, Issue 13, 2004, Pages 5946-5961

Calculating potentials of mean force from steered molecular dynamics simulations

Author keywords

[No Author keywords available]

Indexed keywords

BIMOLECULAR SYSTEMS; STEERED MOLECULAR DYNAMICS (SMD);

EID: 4143087050     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1651473     Document Type: Review
Times cited : (751)

References (52)
  • 29
    • 16544385784 scopus 로고    scopus 로고
    • note
    • In thermodynamics, the term isothermal usually means that the temperature of the system remains constant during the process. Here we use the term to mean that the system is in contact with a bath at constant temperature, though the temperature of the system is not necessarily constant during the process. In fact, the system's temperature is not even defined when we deal with nonequilibrium processes. The same applies to the term isobaric.
  • 30
    • 0032023968 scopus 로고    scopus 로고
    • Generalization of Jarzynski's equality to the isobaric-isothermal ensemble was discussed in G. E. Crooks, J. Stat. Phys. 90, 1481 (1998).
    • (1998) J. Stat. Phys. , vol.90 , pp. 1481
    • Crooks, G.E.1
  • 36
    • 1542347541 scopus 로고    scopus 로고
    • There is a third type of method, such as the isokinetic Gaussian thermostat, in which equations of motion are modified by the addition of deterministic terms, but without introducing new degrees of freedom. The nonequilibrium work relation has been established for the isokinetic Gaussian thermostat. See, D. J. Evans, Mol. Phys. 101, 1551 (2003).
    • (2003) Mol. Phys. , vol.101 , pp. 1551
    • Evans, D.J.1
  • 44
    • 16544393243 scopus 로고    scopus 로고
    • O. Mazonka and C. Jarzynski, cond-mat/9912121 (1999)
    • O. Mazonka and C. Jarzynski, cond-mat/9912121 (1999).
  • 46
    • 16544394986 scopus 로고    scopus 로고
    • note
    • c.
  • 50
    • 16544394815 scopus 로고    scopus 로고
    • note
    • Recall that the Gaussian nature of the work distribution depends on the assumption of the overdamped Langevin equation (Sec. III D). It is desirable to test this assumption in simulations.
  • 52
    • 16544394469 scopus 로고    scopus 로고
    • note
    • One way of doing this is the Langevin piston method, which is introduced in Sec. II G.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.