메뉴 건너뛰기




Volumn 33, Issue 1-2, 2007, Pages 47-56

Generalized-ensemble algorithms for molecular dynamics simulations

Author keywords

Generalized ensemble algorithms; Molecular dynamics simulation; Multibaric multithermal algorithm; Multicanonical algorithm; Multioverlap algorithm

Indexed keywords

COMPUTER SIMULATION; DEGREES OF FREEDOM (MECHANICS); LARGE SCALE SYSTEMS; MOLECULAR DYNAMICS; MONTE CARLO METHODS; POTENTIAL ENERGY;

EID: 33947414877     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927020601096812     Document Type: Conference Paper
Times cited : (33)

References (53)
  • 1
    • 84943502952 scopus 로고
    • A molecular dynamics method for simulations in the canonical ensemble
    • S. Nosé. A molecular dynamics method for simulations in the canonical ensemble. Mol. Phys., 52, 255 (1984).
    • (1984) Mol. Phys , vol.52 , pp. 255
    • Nosé, S.1
  • 2
    • 34547809547 scopus 로고
    • A unified formulation of the constant temperature molecular dynamics methods
    • S. Nosé. A unified formulation of the constant temperature molecular dynamics methods. J. Chem. Phys., 81, 511 (1984).
    • (1984) J. Chem. Phys , vol.81 , pp. 511
    • Nosé, S.1
  • 4
    • 36749107785 scopus 로고
    • Molecular dyanmics simulations at constant pressure and/or temperature
    • H.C. Andersen. Molecular dyanmics simulations at constant pressure and/or temperature. J. Chem. Phys., 72, 2384 (1980).
    • (1980) J. Chem. Phys , vol.72 , pp. 2384
    • Andersen, H.C.1
  • 5
    • 0000617302 scopus 로고
    • High-strain-rate plastic flow studied via nonequilibrium molecular dynamics
    • W.G. Hoover, A.J.C. Ladd, B. Moran. High-strain-rate plastic flow studied via nonequilibrium molecular dynamics, Phys. Rev Lett., 48, 1818 (1982).
    • (1982) Phys. Rev Lett , vol.48 , pp. 1818
    • Hoover, W.G.1    Ladd, A.J.C.2    Moran, B.3
  • 6
    • 36749108497 scopus 로고
    • Computer "experiment" for nonlinear thermodynamics of Couette flow
    • D.J. Evans. Computer "experiment" for nonlinear thermodynamics of Couette flow. J. Chem. Phys., 78, 3297 (1983).
    • (1983) J. Chem. Phys , vol.78 , pp. 3297
    • Evans, D.J.1
  • 7
    • 0001538909 scopus 로고
    • Canonical dynamics: Equilibrium phase-space distributions
    • W.G. Hoover. Canonical dynamics: equilibrium phase-space distributions. Phys. Rev. A, 31, 1695 (1985).
    • (1985) Phys. Rev. A , vol.31 , pp. 1695
    • Hoover, W.G.1
  • 8
    • 36449000062 scopus 로고
    • Nosé-Hoover chains: The canonical ensemble via continuous dynamics
    • G.J. Martyna. M.L. Klein, M. Tuckerman. Nosé-Hoover chains: the canonical ensemble via continuous dynamics. J. Chem. Phys., 97, 2635 (1992).
    • (1992) J. Chem. Phys , vol.97 , pp. 2635
    • Martyna, G.J.1    Klein, M.L.2    Tuckerman, M.3
  • 9
    • 0002674261 scopus 로고
    • NPT-ensemble Monte Carlo calculations for binary liquid mixtures
    • T.R. McDonald. NPT-ensemble Monte Carlo calculations for binary liquid mixtures. Mol. Phys., 23, 41 (1972).
    • (1972) Mol. Phys , vol.23 , pp. 41
    • McDonald, T.R.1
  • 10
    • 26144434487 scopus 로고
    • Crystal structure and pair potentials: A molecular-dynamics study
    • M. Parrinello, A. Rahman. Crystal structure and pair potentials: a molecular-dynamics study. Phys. Rev. Lett., 45, 1199 (1980).
    • (1980) Phys. Rev. Lett , vol.45 , pp. 1199
    • Parrinello, M.1    Rahman, A.2
  • 11
    • 0000728974 scopus 로고
    • Molecular dynamics at constant pressure and temperature
    • D.M. Heyes. Molecular dynamics at constant pressure and temperature. Chem. Phys., 82, 285 (1983).
    • (1983) Chem. Phys , vol.82 , pp. 285
    • Heyes, D.M.1
  • 12
    • 33646645973 scopus 로고
    • Constant-pressure equation of motion
    • W.G. Hoover. Constant-pressure equation of motion. Phys. Rev. A, 34, 2499 (1986).
    • (1986) Phys. Rev. A , vol.34 , pp. 2499
    • Hoover, W.G.1
  • 13
    • 36449003554 scopus 로고
    • Constant pressure molecular dynamics algorithms
    • G.J. Martyna, D.J. Tobias, M.L. Klein. Constant pressure molecular dynamics algorithms. J. Chem. Phys., 101, 4177 (1994).
    • (1994) J. Chem. Phys , vol.101 , pp. 4177
    • Martyna, G.J.1    Tobias, D.J.2    Klein, M.L.3
  • 14
    • 0034864528 scopus 로고    scopus 로고
    • Generalized-ensemble algorithms for molecular simulations of biopolymers
    • A. Mitsutake, Y. Sugita, Y. Okamoto. Generalized-ensemble algorithms for molecular simulations of biopolymers. Biopolymers (Peptide Science), 60, 96 (2001).
    • (2001) Biopolymers (Peptide Science) , vol.60 , pp. 96
    • Mitsutake, A.1    Sugita, Y.2    Okamoto, Y.3
  • 15
    • 1942455272 scopus 로고    scopus 로고
    • Generalized-ensemble algorithms: Enhanced sampling techniques for Monte Carlo and molecular dynamics simulations
    • Y. Okamoto. Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations. J. Mol. Graphics Mod., 22, 425 (2004).
    • (2004) J. Mol. Graphics Mod , vol.22 , pp. 425
    • Okamoto, Y.1
  • 16
    • 0000106469 scopus 로고
    • Multicanonical algorithms for first order phase transitions
    • B.A. Berg, T. Neuhaus. Multicanonical algorithms for first order phase transitions. Phys. Lett., B267, 249 (1991).
    • (1991) Phys. Lett , vol.B267 , pp. 249
    • Berg, B.A.1    Neuhaus, T.2
  • 17
    • 4243613377 scopus 로고
    • Multicanonical ensemble: A new approach to simulate first-order phase transitions
    • B.A. Berg, T. Neuhaus. Multicanonical ensemble: a new approach to simulate first-order phase transitions. Phys. Rev. Lett., 68, 9 (1992).
    • (1992) Phys. Rev. Lett , vol.68 , pp. 9
    • Berg, B.A.1    Neuhaus, T.2
  • 19
    • 0001629677 scopus 로고
    • New approach to spin-glass simulations
    • B.A. Berg, T. Celik, New approach to spin-glass simulations. Phys. Rev. Lett., 69, 2292 (1992).
    • (1992) Phys. Rev. Lett , vol.69 , pp. 2292
    • Berg, B.A.1    Celik, T.2
  • 20
    • 0002307060 scopus 로고
    • Simulation of an ensemble with varying magnetic field: A nemerical determination of the first-order interface tension in the D = 2 Ising model
    • B.A. Berg, U.H.E. Hansmann, T. Neuhaus. Simulation of an ensemble with varying magnetic field: a nemerical determination of the first-order interface tension in the D = 2 Ising model. Phys. Rev B, 47, 497 (1993).
    • (1993) Phys. Rev B , vol.47 , pp. 497
    • Berg, B.A.1    Hansmann, U.H.E.2    Neuhaus, T.3
  • 21
    • 0001597074 scopus 로고
    • Multibondic cluster algorithm for Monte Carlo simulations of first-order phase transitions
    • W. Janke, S. Kappler. Multibondic cluster algorithm for Monte Carlo simulations of first-order phase transitions. Phys. Rev. Lett., 74, 212 (1995).
    • (1995) Phys. Rev. Lett , vol.74 , pp. 212
    • Janke, W.1    Kappler, S.2
  • 22
    • 0001046145 scopus 로고    scopus 로고
    • Multioverlap simulations of the 3D Edwards-Anderson Ising spin glass
    • B.A. Berg, W. Janke. Multioverlap simulations of the 3D Edwards-Anderson Ising spin glass. Phys. Rev Lett., 80, 4771 (1998).
    • (1998) Phys. Rev Lett , vol.80 , pp. 4771
    • Berg, B.A.1    Janke, W.2
  • 23
    • 0000786630 scopus 로고    scopus 로고
    • Spin-glass overlap barriers in three and four dimensions
    • B.A. Berg, A. Billoire, W. Janke. Spin-glass overlap barriers in three and four dimensions. Phys. Rev. B, 61, 12143 (2000).
    • (2000) Phys. Rev. B , vol.61 , pp. 12143
    • Berg, B.A.1    Billoire, A.2    Janke, W.3
  • 24
    • 0034337392 scopus 로고    scopus 로고
    • N. Hatano, J.E. Gubernatis. A multicanonical Monte Carlo study of the 3D (J spin glass. Prog. Theor. Phys. (Suppl.), 138, 442 (2000).
    • N. Hatano, J.E. Gubernatis. A multicanonical Monte Carlo study of the 3D (J spin glass. Prog. Theor. Phys. (Suppl.), 138, 442 (2000).
  • 25
    • 5244260010 scopus 로고
    • Prediction of peptide conformation by multicanonical algorithms: New approach to the multipleminima problem
    • U.H.E. Hansmann, Y. Okamoto. Prediction of peptide conformation by multicanonical algorithms: new approach to the multipleminima problem. J. Comput. Chem., 14, 1333 (1993).
    • (1993) J. Comput. Chem , vol.14 , pp. 1333
    • Hansmann, U.H.E.1    Okamoto, Y.2
  • 26
    • 0030572603 scopus 로고    scopus 로고
    • Molecular dynamics Langevin and hybrid Monte Carlo simulations in a multicanonical ensemble
    • U.H.E. Hansmann, Y. Okamoto, F. Eisenmenger. Molecular dynamics Langevin and hybrid Monte Carlo simulations in a multicanonical ensemble. Chem. Phys. Lett., 259, 321 (1996).
    • (1996) Chem. Phys. Lett , vol.259 , pp. 321
    • Hansmann, U.H.E.1    Okamoto, Y.2    Eisenmenger, F.3
  • 27
    • 0030819348 scopus 로고    scopus 로고
    • Multicanonical ensemble generated by molecular dynamics simulation for enhanced conformational sampling of peptides
    • N. Nakajima, H. Nakamura, A. Kidera. Multicanonical ensemble generated by molecular dynamics simulation for enhanced conformational sampling of peptides. J Phys. Chem. B, 101, 817 (1997).
    • (1997) J Phys. Chem. B , vol.101 , pp. 817
    • Nakajima, N.1    Nakamura, H.2    Kidera, A.3
  • 28
    • 0031648813 scopus 로고    scopus 로고
    • Probability distributions for complex systems: Adaptive umbrella sampling of the potential energy
    • C. Bartels, M. Karplus. Probability distributions for complex systems: adaptive umbrella sampling of the potential energy. J. Phys. Chem. B, 102, 865 (1998).
    • (1998) J. Phys. Chem. B , vol.102 , pp. 865
    • Bartels, C.1    Karplus, M.2
  • 29
    • 0005248491 scopus 로고
    • Method to study relaxation of metastable phases: Macroscopic mean-field dynamics
    • J. Lee, M.A. Novotny, P.A. Rikvold. Method to study relaxation of metastable phases: macroscopic mean-field dynamics. Phys. Rev. E, 52, 356(1995).
    • (1995) Phys. Rev. E , vol.52 , pp. 356
    • Lee, J.1    Novotny, M.A.2    Rikvold, P.A.3
  • 30
    • 0001186767 scopus 로고    scopus 로고
    • Method for free-energy calculations using iterative techniques
    • S. Kumar, P. Payne, M. Vásquez. Method for free-energy calculations using iterative techniques. J. Comput. Chem., 17, 1269(1996).
    • (1996) J. Comput. Chem , vol.17 , pp. 1269
    • Kumar, S.1    Payne, P.2    Vásquez, M.3
  • 31
    • 4344606960 scopus 로고    scopus 로고
    • Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations
    • C. Bartels, M. Karplus. Multidimensional adaptive umbrella sampling: applications to main chain and side chain peptide conformations. J. Comput. Chem., 18, 1450 (1997).
    • (1997) J. Comput. Chem , vol.18 , pp. 1450
    • Bartels, C.1    Karplus, M.2
  • 32
    • 0001738980 scopus 로고    scopus 로고
    • Two-component multicanonical Monte Carlo method for effective conformational sampling
    • J. Higo, N. Nakajima, H. Shirai, A. Kidera, H. Nakamura. Two-component multicanonical Monte Carlo method for effective conformational sampling. J. Comput. Chem., 18, 2086 (1997).
    • (1997) J. Comput. Chem , vol.18 , pp. 2086
    • Higo, J.1    Nakajima, N.2    Shirai, H.3    Kidera, A.4    Nakamura, H.5
  • 33
    • 0032285722 scopus 로고    scopus 로고
    • Simulation of lattice polymers with multi-self-overlap ensemble
    • Y. Iba, G. Chikenji, M. Kikuchi. Simulation of lattice polymers with multi-self-overlap ensemble. J. Phys. Soc. Jpn., 67, 3327 (1998).
    • (1998) J. Phys. Soc. Jpn , vol.67 , pp. 3327
    • Iba, Y.1    Chikenji, G.2    Kikuchi, M.3
  • 34
    • 0242579552 scopus 로고    scopus 로고
    • Multioverlap simulations for transitions between reference configurations
    • B.A. Berg, H. Noguchi, Y. Okamoto. Multioverlap simulations for transitions between reference configurations. Phys. Rev. E, 68, 036126 (2003).
    • (2003) Phys. Rev. E , vol.68 , pp. 036126
    • Berg, B.A.1    Noguchi, H.2    Okamoto, Y.3
  • 35
    • 10344247635 scopus 로고    scopus 로고
    • Multi-overlap molecular dynamics methods for biomolecular systems
    • S.G. Itoh, Y. Okamoto. Multi-overlap molecular dynamics methods for biomolecular systems. Chem. Phys. Lett., 400, 308 (2004).
    • (2004) Chem. Phys. Lett , vol.400 , pp. 308
    • Itoh, S.G.1    Okamoto, Y.2
  • 36
    • 34547648709 scopus 로고    scopus 로고
    • Theoretical studies of transition states by the multioverlap molecular dynamics methods
    • S.G. Itoh, Y. Okamoto. Theoretical studies of transition states by the multioverlap molecular dynamics methods. J. Chem. Phys., 124, 104103 (2006).
    • (2006) J. Chem. Phys , vol.124 , pp. 104103
    • Itoh, S.G.1    Okamoto, Y.2
  • 37
    • 1642534558 scopus 로고    scopus 로고
    • Monte Carlo simulations in multibaric- multithermal ensemble
    • H. Okumura, Y. Okamoto. Monte Carlo simulations in multibaric- multithermal ensemble. Chem. Phys. Lett., 383, 391 (2004).
    • (2004) Chem. Phys. Lett , vol.383 , pp. 391
    • Okumura, H.1    Okamoto, Y.2
  • 38
    • 42749101256 scopus 로고    scopus 로고
    • Monte Carlo simulations in generalized isobaric-isothermal ensembles
    • H. Okumura, Y. Okamoto. Monte Carlo simulations in generalized isobaric-isothermal ensembles. Phys. Rev. E, 70, 026702 (2004).
    • (2004) Phys. Rev. E , vol.70 , pp. 026702
    • Okumura, H.1    Okamoto, Y.2
  • 39
    • 20444459163 scopus 로고    scopus 로고
    • Liquid-gas phase transitions studied by multibaric-multithermal Monte Carlo simulations
    • H. Okumura, Y. Okamoto. Liquid-gas phase transitions studied by multibaric-multithermal Monte Carlo simulations. J. Phys. Soc. Jpn., 73, 3304 (2004).
    • (2004) J. Phys. Soc. Jpn , vol.73 , pp. 3304
    • Okumura, H.1    Okamoto, Y.2
  • 40
    • 2942550984 scopus 로고    scopus 로고
    • Molecular dynamics simulation in the multibaric-multithermal ensemble
    • H. Okumura, Y. Okamoto, Molecular dynamics simulation in the multibaric-multithermal ensemble. Chem. Phys. Lett., 391, 248 (2004).
    • (2004) Chem. Phys. Lett , vol.391 , pp. 248
    • Okumura, H.1    Okamoto, Y.2
  • 41
    • 32444434410 scopus 로고    scopus 로고
    • Multibaric-multithermal ensemble molecular dynamics simulations
    • H. Okumura, Y. Okamoto. Multibaric-multithermal ensemble molecular dynamics simulations. J. Comput. Chem., 27, 379 (2006).
    • (2006) J. Comput. Chem , vol.27 , pp. 379
    • Okumura, H.1    Okamoto, Y.2
  • 42
    • 4243819810 scopus 로고
    • New Monte Carlo technique for studying phase transitions
    • A.M. Ferrenberg, R.H. Swendsen. New Monte Carlo technique for studying phase transitions. Phys. Rev. Lett., 61, 2635 (1988):
    • (1988) Phys. Rev. Lett , vol.61 , pp. 2635
    • Ferrenberg, A.M.1    Swendsen, R.H.2
  • 43
    • 33947408162 scopus 로고    scopus 로고
    • ibid. 63, 1658 (1989).
    • ibid. 63, 1658 (1989).
  • 45
    • 33947418952 scopus 로고    scopus 로고
    • Effective sampling in the configurational space by the multicanonical-multioverlap algorithm, e-print: Condmat/0610169
    • submitted for publication
    • S.G. Itoh, Y. Okamoto. Effective sampling in the configurational space by the multicanonical-multioverlap algorithm, e-print: condmat/0610169, submitted for publication.
    • Itoh, S.G.1    Okamoto, Y.2
  • 46
    • 0041784950 scopus 로고    scopus 로고
    • 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. Stole, J. Straub, M. Watanabe, J. Wiórkiewicz-Kuczera, D. Yin, M. Karplus. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B, 102, 3586 (1998).
    • 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. Stole, J. Straub, M. Watanabe, J. Wiórkiewicz-Kuczera, D. Yin, M. Karplus. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B, 102, 3586 (1998).
  • 49
    • 0034317069 scopus 로고    scopus 로고
    • Liquid-vapor coexistence curves of several interatomic model potentials
    • H. Okumura, F. Yonezawa, Liquid-vapor coexistence curves of several interatomic model potentials. J. Chem. Phys., 113, 9162 (2000).
    • (2000) J. Chem. Phys , vol.113 , pp. 9162
    • Okumura, H.1    Yonezawa, F.2
  • 50
    • 23044527417 scopus 로고    scopus 로고
    • Reliable determination of the liquid-vapor critical point by the NVT plus test particle method
    • H. Okumura, F. Yonezawa. Reliable determination of the liquid-vapor critical point by the NVT plus test particle method. J. Phys. Soc. Jpn., 70, 1990 (2001).
    • (2001) J. Phys. Soc. Jpn , vol.70 , pp. 1990
    • Okumura, H.1    Yonezawa, F.2
  • 51
    • 0001471515 scopus 로고    scopus 로고
    • The Nosé-Poincaré method for constant temperture molecular dynamics
    • S.D. Bond, B.J. Leimkuhler, B.B. Laird. The Nosé-Poincaré method for constant temperture molecular dynamics. J. Comput. Phys., 151, 114 (1999).
    • (1999) J. Comput. Phys , vol.151 , pp. 114
    • Bond, S.D.1    Leimkuhler, B.J.2    Laird, B.B.3
  • 52
    • 0035585460 scopus 로고    scopus 로고
    • An improved symplectic integrator for Nosé- Poincaré thermostat
    • S. Nose. An improved symplectic integrator for Nosé- Poincaré thermostat. J. Phys. Soc. Jpn., 70, 75 (2001).
    • (2001) J. Phys. Soc. Jpn , vol.70 , pp. 75
    • Nose, S.1
  • 53
    • 33947383771 scopus 로고    scopus 로고
    • Explicit symplectic integrators of molecular dynamics algorithms for rigid-body molecules in the canonical, isothermal-isobaric, and related ensembles
    • e-print: cond-mat/0610382, submitted for publication
    • H. Okumura, S.G. Itoh, Y. Okamoto. Explicit symplectic integrators of molecular dynamics algorithms for rigid-body molecules in the canonical, isothermal-isobaric, and related ensembles, e-print: cond-mat/0610382, submitted for publication.
    • Okumura, H.1    Itoh, S.G.2    Okamoto, Y.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.