-
13
-
-
0028715070
-
-
10.1080/08927029408021983
-
T. Forester and W. Smith, Mol. Simul. 13, 195 (1994). 10.1080/08927029408021983
-
(1994)
Mol. Simul.
, vol.13
, pp. 195
-
-
Forester, T.1
Smith, W.2
-
14
-
-
84963146276
-
-
10.1080/08927029108022142
-
H. Grubmller, H. Heller, A. Windemuth, and K. Schulten, Mol. Simul. 6, 121 (1991). 10.1080/08927029108022142
-
(1991)
Mol. Simul.
, vol.6
, pp. 121
-
-
Grubmller, H.1
Heller, H.2
Windemuth, A.3
Schulten, K.4
-
18
-
-
0034817509
-
Langevin stabilization of molecular dynamics
-
DOI 10.1063/1.1332996
-
J. A. Izaguirre, D. P. Catarello, J. M. Wozniak, and R. D. Skeel, J. Chem. Phys. 114, 2090 (2001). 10.1063/1.1332996 (Pubitemid 32873171)
-
(2001)
Journal of Chemical Physics
, vol.114
, Issue.5
, pp. 2090-2098
-
-
Lzaguirre, J.A.1
Catarello, D.P.2
Wozniak, J.M.3
Skeel, R.D.4
-
19
-
-
0037147531
-
-
10.1080/0026897021000018321
-
R. D. Skeel and J. A. Izaguirre, Mol. Phys. 100, 3885 (2002). 10.1080/0026897021000018321
-
(2002)
Mol. Phys.
, vol.100
, pp. 3885
-
-
Skeel, R.D.1
Izaguirre, J.A.2
-
20
-
-
34547591762
-
Design of quasisymplectic propagators for Langevin dynamics
-
DOI 10.1063/1.2753496
-
S. Melchionna, J. Chem. Phys. 127, 044108 (2007). 10.1063/1.2753496 (Pubitemid 47192043)
-
(2007)
Journal of Chemical Physics
, vol.127
, Issue.4
, pp. 044108
-
-
Melchionna, S.1
-
24
-
-
0000219318
-
Overcoming stability limitations in biomolecular dynamics. I. Combining force splitting via extrapolation with Langevin dynamics in LN
-
DOI 10.1063/1.476736, PII S0021960698502206
-
E. Barth and T. Schlick, J. Chem. Phys. 109, 1617 (1998). 10.1063/1.476736 (Pubitemid 128678029)
-
(1998)
Journal of Chemical Physics
, vol.109
, Issue.5
, pp. 1617-1632
-
-
Barth, E.1
Schlick, T.2
-
28
-
-
0000026966
-
-
10.1080/00268979600100761
-
G. J. Martyna, M. E. Tuckerman, D. J. Tobias, and M. L. Klein, Mol. Phys. 87, 1117 (1996). 10.1080/00268979600100761
-
(1996)
Mol. Phys.
, vol.87
, pp. 1117
-
-
Martyna, G.J.1
Tuckerman, M.E.2
Tobias, D.J.3
Klein, M.L.4
-
30
-
-
0034597299
-
-
10.1016/S0166-1280(99)00314-0
-
J. Komeiji, J. Mol. Struct.: THEOCHEM 530, 237 (2000). 10.1016/S0166-1280(99)00314-0
-
(2000)
J. Mol. Struct.: THEOCHEM
, vol.530
, pp. 237
-
-
Komeiji, J.1
-
32
-
-
0942299442
-
-
10.1063/1.1629675
-
S. A. Chin, J. Chem. Phys. 120, 8 (2004). 10.1063/1.1629675
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 8
-
-
Chin, S.A.1
-
34
-
-
33947266386
-
-
Lecture Notes in Physics Vol. 703, (Springer-Verlag, Berlin), Vol. 1.
-
J. B. Abrams, M. E. Tuckerman, and G. J. Martyna, Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology, Lecture Notes in Physics Vol. 703, p. 139 (Springer-Verlag, Berlin, 2006), Vol. 1.
-
(2006)
Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology
, pp. 139
-
-
Abrams, J.B.1
Tuckerman, M.E.2
Martyna, G.J.3
-
35
-
-
70349298628
-
-
10.1063/1.3212922
-
I. P. Omelyan, J. Chem. Phys. 131, 104101 (2009). 10.1063/1.3212922
-
(2009)
J. Chem. Phys.
, vol.131
, pp. 104101
-
-
Omelyan, I.P.1
-
38
-
-
0008985494
-
Extrapolation versus impulse in multiple-timestepping schemes. II. Linear analysis and applications to Newtonian and Langevin dynamics
-
DOI 10.1063/1.476737, PII S0021960698503200
-
E. Barth and T. Schlick, J. Chem. Phys. 109, 1633 (1998). 10.1063/1.476737 (Pubitemid 128678030)
-
(1998)
Journal of Chemical Physics
, vol.109
, Issue.5
, pp. 1633-1642
-
-
Barth, E.1
Schlick, T.2
-
40
-
-
0001310692
-
Nonlinear Resonance Artifacts in Molecular Dynamics Simulations
-
DOI 10.1006/jcph.1998.5879, PII S002199919895879X
-
T. Schlick, M. Mandziuk, R. D. Skeel, and K. Srinivas, J. Comput. Phys. 140, 1 (1998). 10.1006/jcph.1998.5879 (Pubitemid 128343260)
-
(1998)
Journal of Computational Physics
, vol.140
, Issue.1
, pp. 1-29
-
-
Schlick, T.1
Mandziuk, M.2
Skeel, R.D.3
Srinivas, K.4
-
42
-
-
48749148224
-
-
10.1016/0021-9991(83)90014-1
-
H. C. Andersen, J. Comput. Phys. 52, 24 (1983). 10.1016/0021-9991(83) 90014-1
-
(1983)
J. Comput. Phys.
, vol.52
, pp. 24
-
-
Andersen, H.C.1
-
45
-
-
0031678359
-
-
10.1063/1.168642
-
I. P. Omelyan, Comput. Phys. 12, 97 (1998). 10.1063/1.168642
-
(1998)
Comput. Phys.
, vol.12
, pp. 97
-
-
Omelyan, I.P.1
-
46
-
-
0032048085
-
-
10.1016/S0010-4655(98)00024-1
-
I. P. Omelyan, Comput. Phys. Commun. 109, 171 (1998). 10.1016/S0010-4655(98)00024-1
-
(1998)
Comput. Phys. Commun.
, vol.109
, pp. 171
-
-
Omelyan, I.P.1
-
47
-
-
0001525343
-
-
10.1103/PhysRevE.58.1169
-
I. P. Omelyan, Phys. Rev. E 58, 1169 (1998). 10.1103/PhysRevE.58.1169
-
(1998)
Phys. Rev. e
, vol.58
, pp. 1169
-
-
Omelyan, I.P.1
-
49
-
-
26844468237
-
-
10.1080/08927029908022097
-
I. P. Omelyan, Mol. Simul. 22, 213 (1999). 10.1080/08927029908022097
-
(1999)
Mol. Simul.
, vol.22
, pp. 213
-
-
Omelyan, I.P.1
-
50
-
-
0037157302
-
Symplectic quaternion scheme for biophysical molecular dynamics
-
DOI 10.1063/1.1473654
-
T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, D. Newns, and G. J. Martyna, J. Chem. Phys. 116, 8649 (2002). 10.1063/1.1473654 (Pubitemid 34631413)
-
(2002)
Journal of Chemical Physics
, vol.116
, Issue.20
, pp. 8649-8659
-
-
Miller III, T.F.1
Eleftheriou, M.2
Pattnaik, P.3
Ndirango, A.4
Newns, D.5
Martyna, G.J.6
-
51
-
-
34547558218
-
Advanced gradientlike methods for rigid-body molecular dynamics
-
DOI 10.1063/1.2753474
-
I. P. Omelyan, J. Chem. Phys. 127, 044102 (2007). 10.1063/1.2753474 (Pubitemid 47192037)
-
(2007)
Journal of Chemical Physics
, vol.127
, Issue.4
, pp. 044102
-
-
Omelyan, I.P.1
-
52
-
-
49449108398
-
-
10.1103/PhysRevE.78.026702
-
I. P. Omelyan, Phys. Rev. E 78, 026702 (2008). 10.1103/PhysRevE.78.026702
-
(2008)
Phys. Rev. e
, vol.78
, pp. 026702
-
-
Omelyan, I.P.1
-
55
-
-
0004016501
-
-
10.1063/1.445869
-
W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 79, 926 (1983). 10.1063/1.445869
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
58
-
-
0001251663
-
-
10.1103/PhysRevB.31.2643
-
K. Toukan and A. Rahman, Phys. Rev. B 31, 2643 (1985). 10.1103/PhysRevB.31.2643
-
(1985)
Phys. Rev. B
, vol.31
, pp. 2643
-
-
Toukan, K.1
Rahman, A.2
-
59
-
-
23444454552
-
The Amber biomolecular simulation programs
-
DOI 10.1002/jcc.20290
-
D. Case, T. Cheatham, T. Darden, H. Gohlke, R. Luo, K. Merz, A. Onufriev, C. Simmerling, B. Wang, and R. Woods, J. Comput. Chem. 26, 1668 (2005). 10.1002/jcc.20290 (Pubitemid 43076180)
-
(2005)
Journal of Computational Chemistry
, vol.26
, Issue.16
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham III, T.E.2
Darden, T.3
Gohlke, H.4
Luo, R.5
Merz Jr., K.M.6
Onufriev, A.7
Simmerling, C.8
Wang, B.9
Woods, R.J.10
-
60
-
-
0035913529
-
Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
-
DOI 10.1021/jp003919d
-
G. A. Kaminski, R. A. Friesner, J. Tirado-Rives, and W. L. Jorgensen, J. Phys. Chem. B 105, 6474 (2001). 10.1021/jp003919d (Pubitemid 35339015)
-
(2001)
Journal of Physical Chemistry B
, vol.105
, Issue.28
, pp. 6474-6487
-
-
Kaminski, G.A.1
Friesner, R.A.2
Tirado-Rives, J.3
Jorgensen, W.L.4
-
61
-
-
0041784950
-
-
10.1021/jp973084f
-
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. Stote, J. Straub, M. Watanabe, J. Wirkiewicz-Kuczera, D. Yin, and M. Karplus, J. Phys. Chem. B 102, 3586 (1998). 10.1021/jp973084f
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586
-
-
Mackerell Jr., A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack Jr., R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-Mccarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Roux, B.20
Schlenkrich, M.21
Smith, J.C.22
Stote, R.23
Straub, J.24
Watanabe, M.25
Wirkiewicz-Kuczera, J.26
Yin, D.27
Karplus, M.28
more..
-
62
-
-
30444448249
-
The GROMOS software for biomolecular simulation: GROMOS05
-
DOI 10.1002/jcc.20303
-
M. Christen, P. H. Hnenberger, D. Bakowies, R. Baron, R. Brgi, D. P. Geerke, T. N. Heinz, M. A. Kastenholz, V. Krutler, C. Oostenbrink, C. Peter, D. Trzesniak, and W. F. van Gunsteren, J. Comput. Chem. 26, 1719 (2005). 10.1002/jcc.20303 (Pubitemid 43076183)
-
(2005)
Journal of Computational Chemistry
, vol.26
, Issue.16
, pp. 1719-1751
-
-
Christen, M.1
Hunenberger, P.H.2
Bakowies, D.3
Baron, R.4
Burgi, R.5
Geerke, D.P.6
Heinz, T.N.7
Kastenholz, M.A.8
Krautler, V.9
Oostenbrink, C.10
Peter, C.11
Trzesniak, D.12
Van Gunsteren, W.F.13
-
63
-
-
84968520470
-
-
10.1090/S0002-9939-1959-0108732-6
-
H. F. Trotter, Proc. Amer. math. Soc. 10, 545 (1959). 10.1090/S0002-9939-1959-0108732-6
-
(1959)
Proc. Amer. Math. Soc.
, vol.10
, pp. 545
-
-
Trotter, H.F.1
-
64
-
-
36749110571
-
-
10.1063/1.442716
-
W. C. Swope, H. C. Andersen, P. H. Berens, and K. R. Wilson, J. Chem. Phys. 76, 637 (1982). 10.1063/1.442716
-
(1982)
J. Chem. Phys.
, vol.76
, pp. 637
-
-
Swope, W.C.1
Andersen, H.C.2
Berens, P.H.3
Wilson, K.R.4
-
65
-
-
33646982851
-
Optimized Verlet-like algorithms for molecular dynamics simulations
-
DOI 10.1103/PhysRevE.65.056706, 056706
-
I. P. Omelyan, I. M. Mryglod, and R. Folk, Phys. Rev. E 65, 056706 (2002). 10.1103/PhysRevE.65.056706 (Pubitemid 40606936)
-
(2002)
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics
, vol.65
, Issue.5
-
-
Omelyan, I.P.1
Mryglod, I.M.2
Folk, R.3
-
67
-
-
0005493531
-
-
10.1063/1.479398
-
R. Kutteh, J. Chem. Phys. 111, 1394 (1999). 10.1063/1.479398
-
(1999)
J. Chem. Phys.
, vol.111
, pp. 1394
-
-
Kutteh, R.1
-
70
-
-
33750587438
-
-
10.1063/1.448118
-
H. J. C. Berendsen, J. P. M. Postma, W. F. v. Gunsteren, A. DiNola, and J. R. Haak, J. Chem. Phys. 81, 3684 (1984). 10.1063/1.448118
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Gunsteren, W.F.V.3
Dinola, A.4
Haak, J.R.5
-
71
-
-
3042738171
-
-
10.1080/00268970410001698937
-
A. Mudia and C. Chakravartya, Mol. Phys. 102, 681 (2004). 10.1080/00268970410001698937
-
(2004)
Mol. Phys.
, vol.102
, pp. 681
-
-
Mudia, A.1
Chakravartya, C.2
-
72
-
-
33846086933
-
Canonical sampling through velocity rescaling
-
DOI 10.1063/1.2408420
-
G. Bussi, D. Donadio, and M. Parrinello, J. Chem. Phys. 126, 014101 (2007). 10.1063/1.2408420 (Pubitemid 46068390)
-
(2007)
Journal of Chemical Physics
, vol.126
, Issue.1
, pp. 014101
-
-
Bussi, G.1
Donadio, D.2
Parrinello, M.3
-
73
-
-
0031362386
-
-
10.1016/S0010-4655(97)00109-4
-
I. P. Omelyan, Comput. Phys. Commun. 107, 113 (1997). 10.1016/S0010-4655(97)00109-4
-
(1997)
Comput. Phys. Commun.
, vol.107
, pp. 113
-
-
Omelyan, I.P.1
-
74
-
-
0035424713
-
Efficient multiple time step method for use with Ewald and particle mesh Ewald for large biomolecular systems
-
DOI 10.1063/1.1385159
-
R. Zhou, E. Harder, H. Xu, and B. J. Berne, J. Chem. Phys. 115, 2348 (2001). 10.1063/1.1385159 (Pubitemid 32742791)
-
(2001)
Journal of Chemical Physics
, vol.115
, Issue.5
, pp. 2348-2358
-
-
Zhou, R.1
Harder, E.2
Xu, H.3
Berne, B.J.4
-
75
-
-
0037041682
-
Efficient multiple-time-step integrators with distance-based force splitting for particle-mesh-Ewald molecular dynamics simulations
-
DOI 10.1063/1.1458542
-
X. Qian and T. Schlick, J. Chem. Phys. 116, 5971 (2002). 10.1063/1.1458542 (Pubitemid 34476555)
-
(2002)
Journal of Chemical Physics
, vol.116
, Issue.14
, pp. 5971-5983
-
-
Qian, X.1
Schlick, T.2
-
76
-
-
33846386224
-
Error and timing analysis of multiple time-step integration methods for molecular dynamics
-
DOI 10.1016/j.cpc.2006.10.005, PII S0010465506003729
-
G. Han, Y. Deng, J. Glimm, and G. Martyna, Comput. Phys. Commun. 176, 271 (2007). 10.1016/j.cpc.2006.10.005 (Pubitemid 46135549)
-
(2007)
Computer Physics Communications
, vol.176
, Issue.4
, pp. 271-291
-
-
Han, G.1
Deng, Y.2
Glimm, J.3
Martyna, G.4
|