-
1
-
-
84943502952
-
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
-
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
-
3
-
-
5744249209
-
Equation of state calculations by fast computing machines
-
N. Metropolis, A.W. Rosenbluth, M.N. Rosenbluth, A.M. Teller, E. Teller. Equation of state calculations by fast computing machines. J. Chem. Phys., 21, 1087 (1953).
-
(1953)
J. Chem. Phys
, vol.21
, pp. 1087
-
-
Metropolis, N.1
Rosenbluth, A.W.2
Rosenbluth, M.N.3
Teller, A.M.4
Teller, E.5
-
4
-
-
36749107785
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
-
ibid. 63, 1658 (1989).
-
ibid. 63, 1658 (1989).
-
-
-
-
45
-
-
33947418952
-
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
-
-
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).
-
-
-
-
47
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S. Swaminathan, M. Karplus. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem., 4, 187(1983).
-
(1983)
J. Comput. Chem
, vol.4
, pp. 187
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
49
-
-
0034317069
-
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
-
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
-
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
-
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
-
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
|