-
1
-
-
0000619629
-
The generalized-ensemble approach for protein folding simulations
-
D. Stauffer (World Scientific, Singapore)
-
U. H. E. Hansmann, and Y. Okamoto, "The generalized-ensemble approach for protein folding simulations," in Annual Reviews of Computational Physics VI, edited by D. Stauffer (World Scientific, Singapore, 1999), pp. 129-157.
-
(1999)
Annual Reviews of Computational Physics VI
, pp. 129-157
-
-
Hansmann, U.H.E.1
Okamoto, Y.2
-
2
-
-
0034864528
-
Generalized-ensemble algorithms for molecular simulations of biopolymers
-
A. Mitsutake, Y. Sugita, and Y. Okamoto, "Generalized-ensemble algorithms for molecular simulations of biopolymers," Biopolymers 60, 96-123 (2001). 10.1002/1097-0282(2001)60:2<96::AID-BIP1007>3.0.CO;2-F
-
(2001)
Biopolymers
, vol.60
, pp. 96-123
-
-
Mitsutake, A.1
Sugita, Y.2
Okamoto, Y.3
-
3
-
-
0037664492
-
Free-energy calculations in protein folding by generalized-ensemble algorithms
-
T. Schlick and H. H. Gan (Springer)
-
Y. Sugita, and Y. Okamoto, "Free-energy calculations in protein folding by generalized-ensemble algorithms," in Lecture Notes in Computational Science and Engineering, edited by T. Schlick and H. H. Gan (Springer, 2002), pp. 304-332. 10.1007/978-3-642-56080-4-13
-
(2002)
Lecture Notes in Computational Science and Engineering
, pp. 304-332
-
-
Sugita, Y.1
Okamoto, Y.2
-
4
-
-
0000106469
-
Multicanonical algorithms for first order phase transitions
-
B. A. Berg and T. Neuhaus, "Multicanonical algorithms for first order phase transitions," Phys. Lett. B 267, 249-253 (1991). 10.1016/0370-2693(91)91256-U
-
(1991)
Phys. Lett. B
, vol.267
, pp. 249-253
-
-
Berg, B.A.1
Neuhaus, T.2
-
5
-
-
4243613377
-
Multicanonical ensemble: A new approach to simulate first-order phase transitions
-
B. A. Berg and T. Neuhaus, "Multicanonical ensemble: A new approach to simulate first-order phase transitions," Phys. Rev. Lett. 68, 9-12 (1992). 10.1103/PhysRevLett.68.9
-
(1992)
Phys. Rev. Lett.
, vol.68
, pp. 9-12
-
-
Berg, B.A.1
Neuhaus, T.2
-
6
-
-
84953648015
-
New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles
-
A. P. Lyubartsev, A. A. Martsinovski, S. V. Shevkunov, and P. N. Vorontsov-Velyaminov, "New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles," J. Chem. Phys. 96, 1776 (1992). 10.1063/1.462133
-
(1992)
J. Chem. Phys.
, vol.96
, pp. 1776
-
-
Lyubartsev, A.P.1
Martsinovski, A.A.2
Shevkunov, S.V.3
Vorontsov-Velyaminov, P.N.4
-
7
-
-
33644899039
-
Simulated tempering: A new Monte Carlo scheme
-
E. Marinari and G. Parisi, "Simulated tempering: A new Monte Carlo scheme," Europhys. Lett. (EPL) 19, 451-458 (1992). 10.1209/0295-5075/19/6/002
-
(1992)
Europhys. Lett. (EPL)
, vol.19
, pp. 451-458
-
-
Marinari, E.1
Parisi, G.2
-
8
-
-
0030516672
-
Exchange Monte Carlo method and application to spin glass simulations
-
K. Hukushima and K. Nemoto, "Exchange Monte Carlo method and application to spin glass simulations," J. Phys. Soc. Jpn. 65, 1604-1608 (1996). 10.1143/JPSJ.65.1604
-
(1996)
J. Phys. Soc. Jpn.
, vol.65
, pp. 1604-1608
-
-
Hukushima, K.1
Nemoto, K.2
-
10
-
-
6644221271
-
Efficient, multiple-range random walk algorithm to calculate the density of states
-
F. Wang and D. P. Landau, "Efficient, multiple-range random walk algorithm to calculate the density of states," Phys. Rev. Lett. 86, 2050-2053 (2001). 10.1103/PhysRevLett.86.2050
-
(2001)
Phys. Rev. Lett.
, vol.86
, pp. 2050-2053
-
-
Wang, F.1
Landau, D.P.2
-
11
-
-
39749147672
-
Determining the density of states for classical statistical models: A random walk algorithm to produce a flat histogram
-
F. Wang and D. P. Landau, "Determining the density of states for classical statistical models: A random walk algorithm to produce a flat histogram," Phys. Rev. E 64, 056101 (2001). 10.1103/PhysRevE.64.056101
-
(2001)
Phys. Rev. e
, vol.64
, pp. 056101
-
-
Wang, F.1
Landau, D.P.2
-
13
-
-
35949020425
-
Replica Monte Carlo simulation of spin-glasses
-
R. H. Swendsen and J.-S. Wang, "Replica Monte Carlo simulation of spin-glasses," Phys. Rev. Lett. 57, 2607-2609 (1986). 10.1103/PhysRevLett.57.2607
-
(1986)
Phys. Rev. Lett.
, vol.57
, pp. 2607-2609
-
-
Swendsen, R.H.1
Wang, J.-S.2
-
14
-
-
22144468047
-
Replica Monte Carlo simulation (Revisited)
-
J.-S. Wang and R. H. Swendsen, "Replica Monte Carlo simulation (Revisited)," Prog. Theor. Phys. Suppl. 157, 317-323 (2005). 10.1143/PTPS.157.317
-
(2005)
Prog. Theor. Phys. Suppl.
, vol.157
, pp. 317-323
-
-
Wang, J.-S.1
Swendsen, R.H.2
-
15
-
-
0001616080
-
Replica-exchange molecular dynamics method for protein folding
-
Y. Sugita and Y. Okamoto, "Replica-exchange molecular dynamics method for protein folding," Chem. Phys. Lett. 314, 141-151 (1999). 10.1016/S0009-2614(99)01123-9
-
(1999)
Chem. Phys. Lett.
, vol.314
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
16
-
-
0034294024
-
Multidimensional replica-exchange method for free-energy calculations
-
Y. Sugita, A. Kitao, and Y. Okamoto, "Multidimensional replica-exchange method for free-energy calculations," J. Chem. Phys. 113, 6042 (2000). 10.1063/1.1308516
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 6042
-
-
Sugita, Y.1
Kitao, A.2
Okamoto, Y.3
-
17
-
-
65549164421
-
From multidimensional replica-exchange method to multidimensional multicanonical algorithm and simulated tempering
-
A. Mitsutake and Y. Okamoto, "From multidimensional replica-exchange method to multidimensional multicanonical algorithm and simulated tempering," Phys. Rev. E 79, 047701 (2009). 10.1103/PhysRevE.79.047701
-
(2009)
Phys. Rev. e
, vol.79
, pp. 047701
-
-
Mitsutake, A.1
Okamoto, Y.2
-
18
-
-
67249165701
-
Multidimensional generalized-ensemble algorithms for complex systems
-
A. Mitsutake and Y. Okamoto, "Multidimensional generalized-ensemble algorithms for complex systems," J. Chem. Phys. 130, 214105 (2009). 10.1063/1.3127783
-
(2009)
J. Chem. Phys.
, vol.130
, pp. 214105
-
-
Mitsutake, A.1
Okamoto, Y.2
-
19
-
-
69949183901
-
Simulated-tempering replica-exchange method for the multidimensional version
-
A. Mitsutake, "Simulated-tempering replica-exchange method for the multidimensional version," J. Chem. Phys. 131, 094105 (2009). 10.1063/1.3204443
-
(2009)
J. Chem. Phys.
, vol.131
, pp. 094105
-
-
Mitsutake, A.1
-
20
-
-
84870458456
-
Simulated tempering and magnetizing: Application of two-dimensional simulated tempering to the two-dimensional Ising model and its crossover
-
T. Nagai and Y. Okamoto, "Simulated tempering and magnetizing: Application of two-dimensional simulated tempering to the two-dimensional Ising model and its crossover," Phys. Rev. E 86, 056705 (2012). 10.1103/PhysRevE.86.056705
-
(2012)
Phys. Rev. e
, vol.86
, pp. 056705
-
-
Nagai, T.1
Okamoto, Y.2
-
21
-
-
0034354036
-
Replica-exchange Monte Carlo Method for Ar fluid
-
T. Nishikawa, H. Ohtsuka, Y. Sugita, M. Mikami, and Y. Okamoto, "Replica-exchange Monte Carlo Method for Ar fluid," Prog. Theor. Phys. Suppl. 138, 270-271 (2000). 10.1143/PTPS.138.270
-
(2000)
Prog. Theor. Phys. Suppl.
, vol.138
, pp. 270-271
-
-
Nishikawa, T.1
Ohtsuka, H.2
Sugita, Y.3
Mikami, M.4
Okamoto, Y.5
-
22
-
-
0000551750
-
Replica-exchange Monte Carlo method for the isobaric-isothermal ensemble
-
T. Okabe, M. Kawata, Y. Okamoto, and M. Mikami, "Replica-exchange Monte Carlo method for the isobaric-isothermal ensemble," Chem. Phys. Lett. 335, 435-439 (2001). 10.1016/S0009-2614(01)00055-0
-
(2001)
Chem. Phys. Lett.
, vol.335
, pp. 435-439
-
-
Okabe, T.1
Kawata, M.2
Okamoto, Y.3
Mikami, M.4
-
23
-
-
37649031797
-
Reversible temperature and pressure denaturation of a protein fragment: A replica exchange molecular dynamics simulation study
-
D. Paschek and A. García, "Reversible temperature and pressure denaturation of a protein fragment: A replica exchange molecular dynamics simulation study," Phys. Rev. Lett. 93, 238105 (2004). 10.1103/PhysRevLett.93.238105
-
(2004)
Phys. Rev. Lett.
, vol.93
, pp. 238105
-
-
Paschek, D.1
García, A.2
-
24
-
-
33646516485
-
Possible generalization of Boltzmann-Gibbs statistics
-
C. Tsallis, "Possible generalization of Boltzmann-Gibbs statistics," J. Stat. Phys. 52, 479-487 (1988). 10.1007/BF01016429
-
(1988)
J. Stat. Phys.
, vol.52
, pp. 479-487
-
-
Tsallis, C.1
-
25
-
-
78049317315
-
Generalized simulated tempering for exploring strong phase transitons
-
J. Kim and J. E. Straub, "Generalized simulated tempering for exploring strong phase transitons," J. Chem. Phys. 133, 154101 (2010). 10.1063/1.3503503
-
(2010)
J. Chem. Phys.
, vol.133
, pp. 154101
-
-
Kim, J.1
Straub, J.E.2
-
26
-
-
1642485164
-
Coarse grained model for semiquantitative lipid simulations
-
S. J. Marrink, A. H. de Vries, and A. E. Mark, "Coarse grained model for semiquantitative lipid simulations," J. Chem. Phys. B 108, 750-760 (2004). 10.1021/jp036508g
-
(2004)
J. Chem. Phys. B
, vol.108
, pp. 750-760
-
-
Marrink, S.J.1
De Vries, A.H.2
Mark, A.E.3
-
27
-
-
34547474332
-
The MARTINI force field: Coarse grained model for biomolecular simulations
-
S. J. Marrink, H. J. Risselada, S. Yefimov, D. P. Tieleman, and A. H. de Vries, "The MARTINI force field: Coarse grained model for biomolecular simulations," J. Phys. Chem. B 111, 7812-7824 (2007). 10.1021/jp071097f
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 7812-7824
-
-
Marrink, S.J.1
Risselada, H.J.2
Yefimov, S.3
Tieleman, D.P.4
De Vries, A.H.5
-
28
-
-
84859200266
-
Replica-exchange molecular dynamics simulation of a lipid bilayer system with a coarse-grained model
-
T. Nagai and Y. Okamoto, "Replica-exchange molecular dynamics simulation of a lipid bilayer system with a coarse-grained model," Mol. Simul. 38, 437-441 (2012). 10.1080/08927022.2011.564172
-
(2012)
Mol. Simul.
, vol.38
, pp. 437-441
-
-
Nagai, T.1
Okamoto, Y.2
-
29
-
-
84856663400
-
Phase behavior of a lipid bilayer system studied by a replica-exchange molecular dynamics simulation
-
T. Nagai, R. Ueoka, and Y. Okamoto, "Phase behavior of a lipid bilayer system studied by a replica-exchange molecular dynamics simulation," J. Phys. Soc. Jpn. 81, 024002 (2012). 10.1143/JPSJ.81.024002
-
(2012)
J. Phys. Soc. Jpn.
, vol.81
, pp. 024002
-
-
Nagai, T.1
Ueoka, R.2
Okamoto, Y.3
-
30
-
-
78149429881
-
PACE force field for protein simulations. 1. Full parameterization of version 1 and verification
-
W. Han, C.-K. Wan, F. Jiang, and Y.-D. Wu, "PACE force field for protein simulations. 1. Full parameterization of version 1 and verification," J. Chem. Theory Comput. 6, 3373-3389 (2010). 10.1021/ct1003127
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 3373-3389
-
-
Han, W.1
Wan, C.-K.2
Jiang, F.3
Wu, Y.-D.4
-
31
-
-
26044480933
-
Mass tensor molecular dynamics
-
C. H. Bennett, "Mass tensor molecular dynamics," J. Comput. Phys. 19, 267-279 (1975). 10.1016/0021-9991(75)90077-7
-
(1975)
J. Comput. Phys.
, vol.19
, pp. 267-279
-
-
Bennett, C.H.1
-
32
-
-
0001652151
-
Mass and step length optimization for the calculation of equilibrium properties by molecular dynamics simulation
-
R. Pomès and J. McCammon, "Mass and step length optimization for the calculation of equilibrium properties by molecular dynamics simulation," Chem. Phys. Lett. 166, 425-428 (1990). 10.1016/0009-2614(90)85055-H
-
(1990)
Chem. Phys. Lett.
, vol.166
, pp. 425-428
-
-
Pomès, R.1
McCammon, J.2
-
33
-
-
0001585978
-
Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems
-
K. A. Feenstra, B. Hess, and H. J. C. Berendsen, "Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems," J. Comput. Chem. 20, 786-798 (1999). 10.1002/(SICI)1096-987X(199906)20:8<786::AID-JCC5>3.0.CO;2-B
-
(1999)
J. Comput. Chem.
, vol.20
, pp. 786-798
-
-
Feenstra, K.A.1
Hess, B.2
Berendsen, H.J.C.3
-
34
-
-
70349895348
-
Increasing the time step with mass scaling in Born-Oppenheimer ab initio QM/MM molecular dynamics simulations
-
H. Zheng, S. Wang, and Y. Zhang, "Increasing the time step with mass scaling in Born-Oppenheimer ab initio QM/MM molecular dynamics simulations," J. Comput. Chem. 30, 2706-2711 (2009). 10.1002/jcc.21296
-
(2009)
J. Comput. Chem.
, vol.30
, pp. 2706-2711
-
-
Zheng, H.1
Wang, S.2
Zhang, Y.3
-
35
-
-
79551585811
-
Ab initio mass tensor molecular dynamics
-
E. Tsuchida, "Ab initio mass tensor molecular dynamics," J. Chem. Phys. 134, 044112 (2011). 10.1063/1.3543898
-
(2011)
J. Chem. Phys.
, vol.134
, pp. 044112
-
-
Tsuchida, E.1
-
36
-
-
0026048380
-
Mass-weighted molecular dynamics simulation and conformational analysis of polypeptide
-
B. Mao, "Mass-weighted molecular dynamics simulation and conformational analysis of polypeptide," Biophys. J. 60, 611-622 (1991). 10.1016/S0006-3495(91)82090-2
-
(1991)
Biophys. J.
, vol.60
, pp. 611-622
-
-
Mao, B.1
-
37
-
-
0026206789
-
Mass-weighted molecular dynamics simulation of cyclic polypeptides
-
B. Mao, G. M. Maggiora, and K. C. Chou, "Mass-weighted molecular dynamics simulation of cyclic polypeptides," Biopolymers 31, 1077-1086 (1991). 10.1002/bip.360310907
-
(1991)
Biopolymers
, vol.31
, pp. 1077-1086
-
-
Mao, B.1
Maggiora, G.M.2
Chou, K.C.3
-
38
-
-
77951109278
-
Replica exchange simulation method using temperature and solvent viscosity
-
P. H. Nguyen, "Replica exchange simulation method using temperature and solvent viscosity," J. Chem. Phys. 132, 144109 (2010). 10.1063/1.3369626
-
(2010)
J. Chem. Phys.
, vol.132
, pp. 144109
-
-
Nguyen, P.H.1
-
39
-
-
78650081823
-
Enhanced conformational sampling of peptides via reduced side-chain and solvent masses
-
I.-C. Lin and M. E. Tuckerman, "Enhanced conformational sampling of peptides via reduced side-chain and solvent masses," J. Phys. Chem. B 114, 15935-15940 (2010). 10.1021/jp109865y
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 15935-15940
-
-
Lin, I.-C.1
Tuckerman, M.E.2
-
40
-
-
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, 255-268 (1984). 10.1080/00268978400101201
-
(1984)
Mol. Phys.
, vol.52
, pp. 255-268
-
-
Nosé, S.1
-
41
-
-
0001538909
-
Canonical dynamics: Equilibrium phase-space distributions
-
W. Hoover, "Canonical dynamics: Equilibrium phase-space distributions," Phys. Rev. A 31, 1695-1697 (1985). 10.1103/PhysRevA.31.1695
-
(1985)
Phys. Rev. A
, vol.31
, pp. 1695-1697
-
-
Hoover, W.1
-
44
-
-
77956249820
-
Replica-exchange molecular dynamics simulations for various constant temperature algorithms
-
Y. Mori and Y. Okamoto, "Replica-exchange molecular dynamics simulations for various constant temperature algorithms," J. Phys. Soc. Jpn. 79, 074001 (2010). 10.1143/JPSJ.79.074001
-
(2010)
J. Phys. Soc. Jpn.
, vol.79
, pp. 074001
-
-
Mori, Y.1
Okamoto, Y.2
-
45
-
-
5744249209
-
Equation of state calculations by fast computing machines
-
N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller, "Equation of state calculations by fast computing machines," J. Chem. Phys. 21, 1087 (1953). 10.1063/1.1699114
-
(1953)
J. Chem. Phys.
, vol.21
, pp. 1087
-
-
Metropolis, N.1
Rosenbluth, A.W.2
Rosenbluth, M.N.3
Teller, A.H.4
Teller, E.5
-
46
-
-
81855228612
-
Replica exchange and expanded ensemble simulations as gibbs sampling: Simple improvements for enhanced mixing
-
J. D. Chodera and M. R. Shirts, "Replica exchange and expanded ensemble simulations as gibbs sampling: Simple improvements for enhanced mixing," J. Chem. Phys. 135, 194110 (2011). 10.1063/1.3660669
-
(2011)
J. Chem. Phys.
, vol.135
, pp. 194110
-
-
Chodera, J.D.1
Shirts, M.R.2
-
47
-
-
77957116477
-
Markov chain Monte Carlo method without detailed balance
-
H. Suwa and S. Todo, "Markov chain Monte Carlo method without detailed balance," Phys. Rev. Lett. 105, 120603 (2010). 10.1103/PhysRevLett.105.120603
-
(2010)
Phys. Rev. Lett.
, vol.105
, pp. 120603
-
-
Suwa, H.1
Todo, S.2
-
48
-
-
84872139913
-
Replica-permutation method with the Suwa-Todo algorithm beyond the replica-exchange method
-
S. G. Itoh and H. Okumura, "Replica-permutation method with the Suwa-Todo algorithm beyond the replica-exchange method," J. Chem. Theory Comput. 9, 570-581 (2013). 10.1021/ct3007919
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 570-581
-
-
Itoh, S.G.1
Okumura, H.2
-
49
-
-
36248955554
-
Optimizing replica exchange moves for molecular dynamics
-
W. Nadler and U. Hansmann, "Optimizing replica exchange moves for molecular dynamics," Phys. Rev. E 76, 057102 (2007). 10.1103/PhysRevE.76.057102
-
(2007)
Phys. Rev. e
, vol.76
, pp. 057102
-
-
Nadler, W.1
Hansmann, U.2
-
50
-
-
0029633168
-
GROMACS: A message-passing parallel molecular dynamics implementation
-
H. Berendsen, D. van der Spoel, and R. van Drunen, "GROMACS: A message-passing parallel molecular dynamics implementation," Comput. Phys. Commun. 91, 43-56 (1995). 10.1016/0010-4655(95)00042-E
-
(1995)
Comput. Phys. Commun.
, vol.91
, pp. 43-56
-
-
Berendsen, H.1
Van Der Spoel, D.2
Van Drunen, R.3
-
51
-
-
0035789518
-
GROMACS 3.0: A package for molecular simulation and trajectory analysis
-
E. Lindahl, B. Hess, and D. van der Spoel, "GROMACS 3.0: a package for molecular simulation and trajectory analysis," J. Mol. Model. 7, 306-317 (2001). 10.1007/s008940100045
-
(2001)
J. Mol. Model.
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
Van Der Spoel, D.3
-
52
-
-
27344454932
-
GROMACS: Fast, flexible, and free
-
D. Van Der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, and H. J. C. Berendsen, "GROMACS: fast, flexible, and free," J. Comput. Chem. 26, 1701-1718 (2005). 10.1002/jcc.20291
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1701-1718
-
-
Van Der Spoel, D.1
Lindahl, E.2
Hess, B.3
Groenhof, G.4
Mark, A.E.5
Berendsen, H.J.C.6
-
53
-
-
84875592758
-
GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit
-
S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl, "GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit," Bioinformatics 29, 845-854 (2013). 10.1093/bioinformatics/btt055
-
(2013)
Bioinformatics
, vol.29
, pp. 845-854
-
-
Pronk, S.1
Páll, S.2
Schulz, R.3
Larsson, P.4
Bjelkmar, P.5
Apostolov, R.6
Shirts, M.R.7
Smith, J.C.8
Kasson, P.M.9
Van Der Spoel, D.10
Hess, B.11
Lindahl, E.12
-
55
-
-
36749107785
-
Molecular dynamics simulations at constant pressure and/or temperature
-
H. C. Andersen, "Molecular dynamics simulations at constant pressure and/or temperature," J. Chem. Phys. 72, 2384 (1980). 10.1063/1.439486
-
(1980)
J. Chem. Phys.
, vol.72
, pp. 2384
-
-
Andersen, H.C.1
-
56
-
-
0000026966
-
Explicit reversible integrators for extended systems dynamics
-
G. J. Martyna, M. E. Tuckerman, D. J. Tobias, and M. L. Klein, "Explicit reversible integrators for extended systems dynamics," Mol. Phys. 87, 1117-1157 (1996). 10.1080/00268979600100761
-
(1996)
Mol. Phys.
, vol.87
, pp. 1117-1157
-
-
Martyna, G.J.1
Tuckerman, M.E.2
Tobias, D.J.3
Klein, M.L.4
-
57
-
-
33847664584
-
Explicit symplectic integrators of molecular dynamics algorithms for rigid-body molecules in the canonical, isobaric-isothermal, and related ensembles
-
H. Okumura, S. G. Itoh, and Y. Okamoto, "Explicit symplectic integrators of molecular dynamics algorithms for rigid-body molecules in the canonical, isobaric-isothermal, and related ensembles," J. Chem. Phys. 126, 084103 (2007). 10.1063/1.2434972
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 084103
-
-
Okumura, H.1
Itoh, S.G.2
Okamoto, Y.3
-
58
-
-
84903362010
-
Decomposition-order effects of time integrator on ensemble averages for the Nosé-Hoover thermostat
-
S. G. Itoh, T. Morishita, and H. Okumura, "Decomposition-order effects of time integrator on ensemble averages for the Nosé-Hoover thermostat," J. Chem. Phys. 139, 064103 (2013). 10.1063/1.4817194
-
(2013)
J. Chem. Phys.
, vol.139
, pp. 064103
-
-
Itoh, S.G.1
Morishita, T.2
Okumura, H.3
-
59
-
-
0031599142
-
Mersenne twister: A 623-dimensionally equidistributed uniform pseudo-random number generator
-
M. Matsumoto and T. Nishimura, "Mersenne twister: a 623-dimensionally equidistributed uniform pseudo-random number generator," ACM Trans. Comput. Biol. Bioinf. 8, 3-30 (1998). 10.1145/272991.272995
-
(1998)
ACM Trans. Comput. Biol. Bioinf.
, vol.8
, pp. 3-30
-
-
Matsumoto, M.1
Nishimura, T.2
-
60
-
-
0034317069
-
Liquid-vapor coexistence curves of several interatomic model potentials
-
H. Okumura and F. Yonezawa, "Liquid-vapor coexistence curves of several interatomic model potentials," J. Chem. Phys. 113, 9162 (2000). 10.1063/1.1320828
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 9162
-
-
Okumura, H.1
Yonezawa, F.2
-
62
-
-
36549102647
-
Error estimates on averages of correlated data
-
H. Flyvbjerg and H. G. Petersen, "Error estimates on averages of correlated data," J. Chem. Phys. 91, 461-466 (1989). 10.1063/1.457480
-
(1989)
J. Chem. Phys.
, vol.91
, pp. 461-466
-
-
Flyvbjerg, H.1
Petersen, H.G.2
-
63
-
-
65249116421
-
Analysis of helix-helix interactions of bacteriorhodopsin by replica-exchange simulations
-
H. Kokubo and Y. Okamoto, "Analysis of helix-helix interactions of bacteriorhodopsin by replica-exchange simulations," Biophys. J. 96, 765-776 (2009). 10.1529/biophysj.108.129015
-
(2009)
Biophys. J.
, vol.96
, pp. 765-776
-
-
Kokubo, H.1
Okamoto, Y.2
|