-
1
-
-
0027955787
-
Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins
-
Abagyan RA, Totrov M. 1994. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J. Mol. Biol. 235:983-1002
-
(1994)
J. Mol. Biol.
, vol.235
, pp. 983-1002
-
-
Abagyan, R.A.1
Totrov, M.2
-
2
-
-
0024609825
-
New methodology for computer-aided modelling of biomolecular structure and dynamics: 2. Local deformations and cycles
-
Abagyan RA, Mazur AK. 1989. New methodology for computer-aided modelling of biomolecular structure and dynamics: 2. Local deformations and cycles. J. Biomol. Struct. Dyn. 6:833-45
-
(1989)
J. Biomol. Struct. Dyn.
, vol.6
, pp. 833-845
-
-
Abagyan, R.A.1
Mazur, A.K.2
-
5
-
-
0029985860
-
An efficient method for sampling the essential subspace of proteins
-
Amadei A, Linssen ABM, deGroot BL, van Aalten DMF, Berendsen HJC. 1996. An efficient method for sampling the essential subspace of proteins. J. Biomol. Struct. Dyn. 13:615-25
-
(1996)
J. Biomol. Struct. Dyn.
, vol.13
, pp. 615-625
-
-
Amadei, A.1
Linssen, A.B.M.2
DeGroot, B.L.3
Van Aalten, D.M.F.4
Berendsen, H.J.C.5
-
6
-
-
48749148224
-
Rattle: A 'velocity' version of the SHAKE algorithm for molecular dynamics calculations
-
Andersen H. 1983. Rattle: a 'velocity' version of the SHAKE algorithm for molecular dynamics calculations. J. Comput. Phys. 52:24-34
-
(1983)
J. Comput. Phys.
, vol.52
, pp. 24-34
-
-
Andersen, H.1
-
7
-
-
33746831036
-
Subspace method for long time scale molecular dynamics
-
Askar A, Space B, Rabitz H. 1995. Subspace method for long time scale molecular dynamics. J. Phys. Chem. 99:7330-38
-
(1995)
J. Phys. Chem.
, vol.99
, pp. 7330-7338
-
-
Askar, A.1
Space, B.2
Rabitz, H.3
-
9
-
-
0029911794
-
Asp. Structuring effects of C-H⋯O hydrogen bonds and long-range hydration forces
-
Asp. Structuring effects of C-H⋯O hydrogen bonds and long-range hydration forces. J. Am. Chem. Soc. 118:1181-89
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 1181-1189
-
-
Auffinger, P.1
Louise-May, S.2
Westhof, E.3
-
10
-
-
84950199216
-
A recursive formulation for constrained mechanical system dynamics: Part I. Open loop systems
-
Bae DS, Haug EJ. 1987. A recursive formulation for constrained mechanical system dynamics: Part I. Open loop systems. Mech. Struct. Mach. 15:359-82
-
(1987)
Mech. Struct. Mach.
, vol.15
, pp. 359-382
-
-
Bae, D.S.1
Haug, E.J.2
-
13
-
-
0004248764
-
A separating framework for increasing the timestep in molecular dynamics
-
ed. WF van Gunsteren, PK Weiner, AJ Wilkinson, Chapter 4. Leiden, The Netherlands: ESCOM
-
Barth E, Mandziuk M, Schlick T. 1997. A separating framework for increasing the timestep in molecular dynamics. In Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications, ed. WF van Gunsteren, PK Weiner, AJ Wilkinson, Chapter 4. Leiden, The Netherlands: ESCOM.
-
(1997)
Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications
-
-
Barth, E.1
Mandziuk, M.2
Schlick, T.3
-
14
-
-
0000705676
-
Thermodynamics and quantum corrections from molecular dynamics for liquid water
-
Berens PH, Mackay DH, White GM, Wilson KR. 1983. Thermodynamics and quantum corrections from molecular dynamics for liquid water. J. Chem. Phys. 79:2375-89
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 2375-2389
-
-
Berens, P.H.1
Mackay, D.H.2
White, G.M.3
Wilson, K.R.4
-
16
-
-
0028727183
-
Modeling biomolecules: Larger scales, longer durations
-
Board JA Jr, Kalé LV, Schulten K, Skeel RD, Schlick T. 1994. Modeling biomolecules: larger scales, longer durations. IEEE Comput. Sci. Eng. 1:19-30
-
(1994)
IEEE Comput. Sci. Eng.
, vol.1
, pp. 19-30
-
-
Board Jr., J.A.1
Kalé, L.V.2
Schulten, K.3
Skeel, R.D.4
Schlick, T.5
-
18
-
-
0027641030
-
Hybrid Monte Carlo simulations theory and initial comparison with molecular dynamics
-
Brass A, Pendleton BJ, Chen Y, Robson B. 1993. Hybrid Monte Carlo simulations theory and initial comparison with molecular dynamics. Biopolymers 33:1307-15
-
(1993)
Biopolymers
, vol.33
, pp. 1307-1315
-
-
Brass, A.1
Pendleton, B.J.2
Chen, Y.3
Robson, B.4
-
19
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. 1983. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4:187-217
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
20
-
-
0000885331
-
Harmonic analysis of large systems. I. Methodology
-
Brooks BR, Janežič D, Karplus M. 1995. Harmonic analysis of large systems. I. Methodology. J. Comput. Chem. 16:1522-42
-
(1995)
J. Comput. Chem.
, vol.16
, pp. 1522-1542
-
-
Brooks, B.R.1
Janežič, D.2
Karplus, M.3
-
21
-
-
0003525155
-
-
New York: Wiley
-
Brooks CL III, Karplus M, Pettitt BM. 1988. Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics, Advances in Chemical Physics LXXI. New York: Wiley
-
(1988)
Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics, Advances in Chemical Physics
, vol.71
-
-
Brooks III, C.L.1
Karplus, M.2
Pettitt, B.M.3
-
22
-
-
48749137581
-
Stochastic boundary conditions for molecular dynamics simulations of ST2 water
-
Brünger AT, Brooks CL III, Karplus M, 1982. Stochastic boundary conditions for molecular dynamics simulations of ST2 water. Chem. Phys. Lett. 105:495-500
-
(1982)
Chem. Phys. Lett.
, vol.105
, pp. 495-500
-
-
Brünger, A.T.1
Brooks III, C.L.2
Karplus, M.3
-
23
-
-
26744435691
-
Simulated annealing applied to crystallographic structure refinement
-
ed. JH Kalivas, Amsterdam, The Netherlands: Elsevier
-
Brünger AT, Rice LM. 1995. Simulated annealing applied to crystallographic structure refinement. In Adaption of Simulated Annealing to Chemical Optimization Problems, ed. JH Kalivas, pp. 259-80. Amsterdam, The Netherlands: Elsevier
-
(1995)
Adaption of Simulated Annealing to Chemical Optimization Problems
, pp. 259-280
-
-
Brünger, A.T.1
Rice, L.M.2
-
24
-
-
0028331255
-
Normal mode analysis of protein dynamics
-
Case DA. 1994. Normal mode analysis of protein dynamics. Curr. Opin. Struct. Biol. 4:385-90
-
(1994)
Curr. Opin. Struct. Biol.
, vol.4
, pp. 385-390
-
-
Case, D.A.1
-
25
-
-
33746314863
-
Symplectic integration of Hamiltonian systems
-
Channell PJ, Scovel C. 1990. Symplectic integration of Hamiltonian systems. Nonlinearity 3:231-59
-
(1990)
Nonlinearity
, vol.3
, pp. 231-259
-
-
Channell, P.J.1
Scovel, C.2
-
27
-
-
0029993330
-
On the sensitivity of MD trajectories to changes in water-protein interaction parameters: The potato carboxypeptidase inhibitor in water as a test case for the GROMOS force field
-
Daura X, Oliva B, Querol E, Avilés FX, Tapia O. 1996. On the sensitivity of MD trajectories to changes in water-protein interaction parameters: the potato carboxypeptidase inhibitor in water as a test case for the GROMOS force field. Proteins Struct. Funct. Gen. 25:89-103
-
(1996)
Proteins Struct. Funct. Gen.
, vol.25
, pp. 89-103
-
-
Daura, X.1
Oliva, B.2
Querol, E.3
Avilés, F.X.4
Tapia, O.5
-
28
-
-
0029052930
-
Long-time integration for peptides by the dynamics driver approach
-
Derreumaux P, Schlick T. 1995. Long-time integration for peptides by the dynamics driver approach. Proteins Struct. Fund. Gen. 21:282-302
-
(1995)
Proteins Struct. Fund. Gen.
, vol.21
, pp. 282-302
-
-
Derreumaux, P.1
Schlick, T.2
-
29
-
-
84986483801
-
A truncated-Newton method adapted for CHARMM and biomolecular applications
-
Derreumaux P, Zhang G, Brooks B, Schlick T. 1994. A truncated-Newton method adapted for CHARMM and biomolecular applications. J. Comput. Chem. 15:532-52
-
(1994)
J. Comput. Chem.
, vol.15
, pp. 532-552
-
-
Derreumaux, P.1
Zhang, G.2
Brooks, B.3
Schlick, T.4
-
31
-
-
0029932611
-
Novel methods for molecular dynamics simulations
-
Elber R. 1996. Novel methods for molecular dynamics simulations. Curr. Opin. Struct. Biol. 6:232-35
-
(1996)
Curr. Opin. Struct. Biol.
, vol.6
, pp. 232-235
-
-
Elber, R.1
-
32
-
-
0027366431
-
How consistent are molecular dynamics simulations? Comparing structure and dynamics in reduced and oxidized Escherichia coli thioredoxin
-
Elofsson A, Nilsson L. 1991. How consistent are molecular dynamics simulations? Comparing structure and dynamics in reduced and oxidized Escherichia coli thioredoxin. J. Mol. Biol. 233:766-80
-
(1991)
J. Mol. Biol.
, vol.233
, pp. 766-780
-
-
Elofsson, A.1
Nilsson, L.2
-
33
-
-
0028715070
-
On multiple time-step algorithms and the Ewald sum
-
Forester T, Smith W. 1994. On multiple time-step algorithms and the Ewald sum. Mol. Simul. 13:195-204
-
(1994)
Mol. Simul.
, vol.13
, pp. 195-204
-
-
Forester, T.1
Smith, W.2
-
34
-
-
0000342374
-
Hybrid Monte Carlo simulations of dense polymer systems
-
Forrest BM, Suter UW. 1994. Hybrid Monte Carlo simulations of dense polymer systems. J. Chem. Phys. 101:2616-19
-
(1994)
J. Chem. Phys.
, vol.101
, pp. 2616-2619
-
-
Forrest, B.M.1
Suter, U.W.2
-
36
-
-
84986483796
-
Variable step molecular dynamics: An exploratory technique for peptides with fixed geometry
-
Gibson KD, Scheraga H. 1990. Variable step molecular dynamics: an exploratory technique for peptides with fixed geometry. J. Comput. Chem. 11:468-86
-
(1990)
J. Comput. Chem.
, vol.11
, pp. 468-486
-
-
Gibson, K.D.1
Scheraga, H.2
-
38
-
-
0001672136
-
Symplectic integrators for large scale molecular dynamics simulations: A comparison of several explicit methods
-
Gray SK, Noid DW, Sumpter BG. 1994. Symplectic integrators for large scale molecular dynamics simulations: a comparison of several explicit methods. J. Chem. Phys. 101:4062-72
-
(1994)
J. Chem. Phys.
, vol.101
, pp. 4062-4072
-
-
Gray, S.K.1
Noid, D.W.2
Sumpter, B.G.3
-
39
-
-
84986492552
-
Long time overdamped Langevin dynamics of molecular chains
-
Grønbech-Jensen N, Doniach S. 1994. Long time overdamped Langevin dynamics of molecular chains. J. Comput. Chem. 15:997-1012
-
(1994)
J. Comput. Chem.
, vol.15
, pp. 997-1012
-
-
Grønbech-Jensen, N.1
Doniach, S.2
-
40
-
-
0000689085
-
Predicting slow structural transitions in macromolecular systems: Conformational flooding
-
Grubmüller H. 1995. Predicting slow structural transitions in macromolecular systems: conformational flooding. Phys. Rev. E 52:2893-906
-
(1995)
Phys. Rev. E
, vol.52
, pp. 2893-2906
-
-
Grubmüller, H.1
-
41
-
-
84963146276
-
Generalized Verlet algorithm for efficient molecular dynamics simulations with long-range interactions
-
Grubmüller H, Heller H, Windemuth A, Schulten K. 1991. Generalized Verlet algorithm for efficient molecular dynamics simulations with long-range interactions. Mol. Simul. 6:121-42
-
(1991)
Mol. Simul.
, vol.6
, pp. 121-142
-
-
Grubmüller, H.1
Heller, H.2
Windemuth, A.3
Schulten, K.4
-
44
-
-
0027517952
-
Unfolding and refolding of the native structure of bovine pancreatic trypsin inhibitor studied by computer simulations
-
Hao MH, Pincus MR, Rackovsky S, Scheraga HA. 1993. Unfolding and refolding of the native structure of bovine pancreatic trypsin inhibitor studied by computer simulations. Biochemistry 32:9614-31
-
(1993)
Biochemistry
, vol.32
, pp. 9614-9631
-
-
Hao, M.H.1
Pincus, M.R.2
Rackovsky, S.3
Scheraga, H.A.4
-
45
-
-
0000504254
-
A multiple-time-step molecular dynamics algorithm for macromolecules
-
Humphreys DE, Friesner RA, Berne BJ. 1994. A multiple-time-step molecular dynamics algorithm for macromolecules. J. Phys. Chem. 98:6885-92
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 6885-6892
-
-
Humphreys, D.E.1
Friesner, R.A.2
Berne, B.J.3
-
46
-
-
0028926875
-
Computational approaches to study protein unfolding: Hen egg white lysozyme as a case study
-
Hünenberger PH, Mark AE, van Gunsteren WF, 1995. Computational approaches to study protein unfolding: hen egg white lysozyme as a case study. Proteins Struct. Funct. Gen. 21:196-213
-
(1995)
Proteins Struct. Funct. Gen.
, vol.21
, pp. 196-213
-
-
Hünenberger, P.H.1
Mark, A.E.2
Van Gunsteren, W.F.3
-
47
-
-
0343470337
-
A combined wormlike chain and bead model for dynamic simulations of long DNA
-
Submitted
-
Jian H, Vologodskii A, Schlick T. 1996. A combined wormlike chain and bead model for dynamic simulations of long DNA. J. Comp. Phys. Submitted
-
(1996)
J. Comp. Phys.
-
-
Jian, H.1
Vologodskii, A.2
Schlick, T.3
-
48
-
-
0029276252
-
An efficient symplectic integration algorithm for molecular dynamics simulations
-
Janežič D, Merzel F. 1995. An efficient symplectic integration algorithm for molecular dynamics simulations. J. Chem. Inf. Comput. Sci. 35:321-26
-
(1995)
J. Chem. Inf. Comput. Sci.
, vol.35
, pp. 321-326
-
-
Janežič, D.1
Merzel, F.2
-
49
-
-
0010353041
-
Implicit Runge-Kutta method for molecular dynamics integration
-
Janežič D, Orel B. 1993. Implicit Runge-Kutta method for molecular dynamics integration. J. Chem. Inf. Comput. Sci. 33:252-57
-
(1993)
J. Chem. Inf. Comput. Sci.
, vol.33
, pp. 252-257
-
-
Janežič, D.1
Orel, B.2
-
50
-
-
0028426291
-
Parallelization of an implicit Runge-Kutta method for molecular dynamics integration
-
Janežič D, Orel B. 1994. Parallelization of an implicit Runge-Kutta method for molecular dynamics integration. J. Chem. Inf. Comp. Sci. 34:641-46
-
(1994)
J. Chem. Inf. Comp. Sci.
, vol.34
, pp. 641-646
-
-
Janežič, D.1
Orel, B.2
-
52
-
-
0001715056
-
The Hamiltonian way for computing Hamiltonian dynamics
-
ed. R Spigler, Dordrecht, The Netherlands: Kluwer Academic
-
Kang F. 1990. The Hamiltonian way for computing Hamiltonian dynamics. In Applied and Industrial Mathematics, ed. R Spigler, pp. 17-35. Dordrecht, The Netherlands: Kluwer Academic
-
(1990)
Applied and Industrial Mathematics
, pp. 17-35
-
-
Kang, F.1
-
53
-
-
0000408065
-
Symplectic numerical integrators in constrained Hamiltonian systems
-
Leimkuhler B, Skeel RD. 1994. Symplectic numerical integrators in constrained Hamiltonian systems. J. Comput. Phys. 112:117-25
-
(1994)
J. Comput. Phys.
, vol.112
, pp. 117-125
-
-
Leimkuhler, B.1
Skeel, R.D.2
-
54
-
-
0343087410
-
Integration methods for molecular dynamics
-
Mathematical Approaches to Biomolecular Structure and Dynamics, ed. JP Mesirov, K Schulten, DW Sumners. New York: Springer-Verlag
-
Leimkuhler BJ, Reich S, Skeel RD. 1996. Integration methods for molecular dynamics. In Mathematical Approaches to Biomolecular Structure and Dynamics, ed. JP Mesirov, K Schulten, DW Sumners. IMA Vol. Math. Appl. 82:161-86. New York: Springer-Verlag
-
(1996)
IMA Vol. Math. Appl.
, vol.82
, pp. 161-186
-
-
Leimkuhler, B.J.1
Reich, S.2
Skeel, R.D.3
-
55
-
-
0026869597
-
Langevin dynamics of peptides: The frictional dependence of isomerization rates of N-acetylalanyl-N′-methylamide
-
Loncharich RJ, Brooks BR, Pastor RW. 1992. Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-acetylalanyl-N′-methylamide. Biopolymers 32:523-35
-
(1992)
Biopolymers
, vol.32
, pp. 523-535
-
-
Loncharich, R.J.1
Brooks, B.R.2
Pastor, R.W.3
-
57
-
-
8244227180
-
Molecular dynamics of geometrically constrained polymer systems in generalized coordinates: Basic formalism
-
Ludovice PJ, Suter UW. 1991. Molecular dynamics of geometrically constrained polymer systems in generalized coordinates: basic formalism. Comput. Polym. Sci. 1:69-79
-
(1991)
Comput. Polym. Sci.
, vol.1
, pp. 69-79
-
-
Ludovice, P.J.1
Suter, U.W.2
-
58
-
-
0007148604
-
Resonance in the dynamics of chemical systems simulated by the implicit-midpoint scheme
-
Mandziuk M, Schlick T. 1995. Resonance in the dynamics of chemical systems simulated by the implicit-midpoint scheme. Chem. Phys. Lett. 237:525-35
-
(1995)
Chem. Phys. Lett.
, vol.237
, pp. 525-535
-
-
Mandziuk, M.1
Schlick, T.2
-
60
-
-
0005574236
-
Symplectic integrators for the multichannel Schrödinger equation
-
Manolopoulos DE, Gray SK. 1995. Symplectic integrators for the multichannel Schrödinger equation. J. Chem. Phys. 102:9214-27
-
(1995)
J. Chem. Phys.
, vol.102
, pp. 9214-9227
-
-
Manolopoulos, D.E.1
Gray, S.K.2
-
62
-
-
36449009301
-
Symplectic reversible integrators: Predictor-corrector methods
-
Martyna GJ, Tuckerman ME. 1995. Symplectic reversible integrators: predictor-corrector methods. J. Chem. Phys. 102:8071-77
-
(1995)
J. Chem. Phys.
, vol.102
, pp. 8071-8077
-
-
Martyna, G.J.1
Tuckerman, M.E.2
-
64
-
-
0024609784
-
New methodology for computer-aided modeling of biomolecular structure and dynamics: 1. Non-cyclic structures
-
Mazur AK, Abagyan RA. 1989. New methodology for computer-aided modeling of biomolecular structure and dynamics: 1. Non-cyclic structures. J. Biomol. Struct. Dyn. 6:815-32
-
(1989)
J. Biomol. Struct. Dyn.
, vol.6
, pp. 815-832
-
-
Mazur, A.K.1
Abagyan, R.A.2
-
65
-
-
0000253286
-
Derivation and testing of explicit equations of motion for polymers described by internal coordinates
-
Mazur AK, Dorofeev VE, Abagyan RA. 1991. Derivation and testing of explicit equations of motion for polymers described by internal coordinates. J. Comput. Phys. 92:261-72
-
(1991)
J. Comput. Phys.
, vol.92
, pp. 261-272
-
-
Mazur, A.K.1
Dorofeev, V.E.2
Abagyan, R.A.3
-
68
-
-
0346653215
-
The accuracy of symplectic integrators
-
McLachlan RI, Atela P. 1992. The accuracy of symplectic integrators. Nonlinearity 5:541-62
-
(1992)
Nonlinearity
, vol.5
, pp. 541-562
-
-
McLachlan, R.I.1
Atela, P.2
-
69
-
-
0041299791
-
The notion of error in Langevin dynamics: 1. Linear analysis
-
Mishra B, Schlick T. 1996. The notion of error in Langevin dynamics: 1. Linear analysis. J. Chem. Phys. 105:299-318
-
(1996)
J. Chem. Phys.
, vol.105
, pp. 299-318
-
-
Mishra, B.1
Schlick, T.2
-
70
-
-
84986440341
-
SETTLE: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
-
Miyamoto S, Kollman PA. 1992. SETTLE: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J. Comput. Chem. 13:952-62
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 952-962
-
-
Miyamoto, S.1
Kollman, P.A.2
-
71
-
-
0142080331
-
Increasing the time step in molecular dynamics
-
Nyberg A, Schlick T. 1992. Increasing the time step in molecular dynamics. Chem. Phys. Lett. 198:538-46
-
(1992)
Chem. Phys. Lett.
, vol.198
, pp. 538-546
-
-
Nyberg, A.1
Schlick, T.2
-
72
-
-
0012021417
-
Calculation of classical trajectories with a very large time step: Formalism and numerical examples
-
Olender R, Elber R. 1996. Calculation of classical trajectories with a very large time step: formalism and numerical examples. J. Chem. Phys. 105:9299-315
-
(1996)
J. Chem. Phys.
, vol.105
, pp. 9299-9315
-
-
Olender, R.1
Elber, R.2
-
73
-
-
0002433133
-
Techniques and applications of Langevin dynamics simulations
-
ed. GR Luckhurst, CA Veracini, Dordrecht, The Netherlands: Kluwer Academic
-
Pastor RW. 1994. Techniques and applications of Langevin dynamics simulations. In The Molecular Dynamics of Liquid Crystals, ed. GR Luckhurst, CA Veracini, pp. 85-138. Dordrecht, The Netherlands: Kluwer Academic
-
(1994)
The Molecular Dynamics of Liquid Crystals
, pp. 85-138
-
-
Pastor, R.W.1
-
74
-
-
84952104504
-
An analysis of the accuracy of Langevin and molecular dynamics algorithms
-
Pastor RW, Brooks BR, Szabo A. 1988. An analysis of the accuracy of Langevin and molecular dynamics algorithms. Mol. Phys. 65:1409-19
-
(1988)
Mol. Phys.
, vol.65
, pp. 1409-1419
-
-
Pastor, R.W.1
Brooks, B.R.2
Szabo, A.3
-
75
-
-
84990557178
-
Molecular dynamics by the backward Euler's method
-
Peskin CS, Schlick T. 1989. Molecular dynamics by the backward Euler's method. Commun. Pure Appl. Math. 42:1001-31
-
(1989)
Commun. Pure Appl. Math.
, vol.42
, pp. 1001-1031
-
-
Peskin, C.S.1
Schlick, T.2
-
77
-
-
0001751511
-
Solvent effects on supercoiled DNA dynamics explored by Langevin dynamics simulations
-
Ramachandran G, Schlick T. 1995. Solvent effects on supercoiled DNA dynamics explored by Langevin dynamics simulations. Phys. Rev. E 51:6188-203
-
(1995)
Phys. Rev. E
, vol.51
, pp. 6188-6203
-
-
Ramachandran, G.1
Schlick, T.2
-
78
-
-
0042787277
-
Beyond optimization: Simulating the dynamics of supercoiled DNA by a macroscopic model
-
Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, ed. PM Pardalos, D Shalloway, G Xue. Providence, RI: Am. Math. Soc.
-
Ramachandran G, Schlick T. 1996. Beyond optimization: simulating the dynamics of supercoiled DNA by a macroscopic model. In Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, ed. PM Pardalos, D Shalloway, G Xue. DIMACS Ser. Discrete Math. Theor. Comput. Sci. 23:215-31. Providence, RI: Am. Math. Soc.
-
(1996)
DIMACS Ser. Discrete Math. Theor. Comput. Sci.
, vol.23
, pp. 215-231
-
-
Ramachandran, G.1
Schlick, T.2
-
79
-
-
0031021521
-
Buckling transitions in superhelical DNA: Dependence on the elastic constants and DNA size
-
Ramachandran G, Schlick T. 1997. Buckling transitions in superhelical DNA: dependence on the elastic constants and DNA size. Biopolymers 41:5-25
-
(1997)
Biopolymers
, vol.41
, pp. 5-25
-
-
Ramachandran, G.1
Schlick, T.2
-
80
-
-
0001787214
-
Smoothed dynamics of highly oscillatory Hamiltonian systems
-
Reich S. 1995. Smoothed dynamics of highly oscillatory Hamiltonian systems. Physica D 89:28-12
-
(1995)
Physica D
, vol.89
, pp. 28-112
-
-
Reich, S.1
-
81
-
-
0043084528
-
Enhancing energy conserving methods
-
Reich S. 1996. Enhancing energy conserving methods. BIT 36:122-34
-
(1996)
BIT
, vol.36
, pp. 122-134
-
-
Reich, S.1
-
82
-
-
0001558971
-
Symplectic integration of constrained Hamiltonian systems by composition methods
-
Reich S. 1996. Symplectic integration of constrained Hamiltonian systems by composition methods. SIAM J. Numer. Anal. 33:475-91
-
(1996)
SIAM J. Numer. Anal.
, vol.33
, pp. 475-491
-
-
Reich, S.1
-
83
-
-
0030122430
-
Torsion dynamics of molecular systems
-
Reich S. 1996. Torsion dynamics of molecular systems. Phys. Rev. E 53:4176-81
-
(1996)
Phys. Rev. E
, vol.53
, pp. 4176-4181
-
-
Reich, S.1
-
84
-
-
8244261888
-
Forecast: Clear weather ahead
-
Winter
-
Reiter C. 1995. Forecast: clear weather ahead. Northwest. Perspect. Winter 23-24
-
(1995)
Northwest. Perspect
, pp. 23-24
-
-
Reiter, C.1
-
85
-
-
0028070557
-
Torsion angle dynamics: Reduced variable conformational sampling enhances crystallographic structure refinement
-
Rice LM, Brünger AT. 1994. Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement. Proteins Struct. Funct. Gen. 19:277-90
-
(1994)
Proteins Struct. Funct. Gen.
, vol.19
, pp. 277-290
-
-
Rice, L.M.1
Brünger, A.T.2
-
86
-
-
0002339446
-
Motion under a strong constraining force
-
Rubin H, Ungar P. 1957. Motion under a strong constraining force. Commun. Pure Appl. Math. 10:65-87
-
(1957)
Commun. Pure Appl. Math.
, vol.10
, pp. 65-87
-
-
Rubin, H.1
Ungar, P.2
-
87
-
-
0020798563
-
A canonical integration technique
-
Ruth RD. 1983. A canonical integration technique. IEEE Trans. Nucl. Sci. 30:2669
-
(1983)
IEEE Trans. Nucl. Sci.
, vol.30
, pp. 2669
-
-
Ruth, R.D.1
-
88
-
-
49549141675
-
Molecular dynamics of liquid n-butane near its boiling point
-
Ryckaert JP, Bellemans A. 1975. Molecular dynamics of liquid n-butane near its boiling point. Chem. Phys. Lett. 30:123-25
-
(1975)
Chem. Phys. Lett.
, vol.30
, pp. 123-125
-
-
Ryckaert, J.P.1
Bellemans, A.2
-
89
-
-
33646940952
-
Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert JP, Ciccotti G, Berendsen HJC. 1977. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23:327-41
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Hjc, B.3
-
91
-
-
80051691482
-
Pursuing Laplace's vision on modern computers
-
Mathematical Applications to Biomolecular Structure and Dynamics, ed. JP Mesirov, K Schulten, DW Sumners. New York: Springer-Verlag
-
Schlick T. 1996. Pursuing Laplace's vision on modern computers. In Mathematical Applications to Biomolecular Structure and Dynamics, ed. JP Mesirov, K Schulten, DW Sumners. IMA Vol. Math. Appl. 82:219-47. New York: Springer-Verlag
-
(1996)
IMA Vol. Math. Appl.
, vol.82
, pp. 219-247
-
-
Schlick, T.1
-
93
-
-
0004308888
-
A multigrid tutorial with applications to molecular dynamics
-
Schlick T, Brandt A. 1996. A multigrid tutorial with applications to molecular dynamics. IEEE Comput. Sci. Eng. 3:78-83
-
(1996)
IEEE Comput. Sci. Eng.
, vol.3
, pp. 78-83
-
-
Schlick, T.1
Brandt, A.2
-
94
-
-
0026824139
-
TNPACK - A truncated Newton minimization package for large-scale problems: I. Algorithm and usage
-
Schlick T, Fogelson A. 1992. TNPACK - a truncated Newton minimization package for large-scale problems: I. Algorithm and usage. ACM Trans. Math. Softw. 14:46-70
-
(1992)
ACM Trans. Math. Softw.
, vol.14
, pp. 46-70
-
-
Schlick, T.1
Fogelson, A.2
-
95
-
-
0026554929
-
Supercoiled DNA energetics and dynamics by computer simulation
-
Schlick T, Olson WK. 1992. Supercoiled DNA energetics and dynamics by computer simulation. J. Mol. Biol. 223:1089-119
-
(1992)
J. Mol. Biol.
, vol.223
, pp. 1089-1119
-
-
Schlick, T.1
Olson, W.K.2
-
96
-
-
84988050306
-
A powerful truncated Newton method for potential energy functions
-
Schlick T, Overton ML. 1987. A powerful truncated Newton method for potential energy functions. J. Comput. Chem. 8:1025-39
-
(1987)
J. Comput. Chem.
, vol.8
, pp. 1025-1039
-
-
Schlick, T.1
Overton, M.L.2
-
97
-
-
84990622745
-
Can classical equations simulate quantum-mechanical behavior? A molecular dynamics investigation of a diatomic molecule with a Morse potential
-
Schlick T, Peskin CS. 1989. Can classical equations simulate quantum-mechanical behavior? A molecular dynamics investigation of a diatomic molecule with a Morse potential. Commun. Pure Appl. Math. 42:1141-63
-
(1989)
Commun. Pure Appl. Math.
, vol.42
, pp. 1141-1163
-
-
Schlick, T.1
Peskin, C.S.2
-
98
-
-
36449007714
-
Comment on: The evaluation of LI and LIN for dynamics simulations
-
Schlick T, Peskin CS. 1995. Comment on: The evaluation of LI and LIN for dynamics simulations. J. Chem. Phys. 103:9888-89
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 9888-9889
-
-
Schlick, T.1
Peskin, C.S.2
-
99
-
-
0027830954
-
Multiple time steps: Limits on the speedup of molecular dynamics simulations of aqueous systems
-
Scully JL, Hermans J. 1993. Multiple time steps: limits on the speedup of molecular dynamics simulations of aqueous systems. Mol. Simul. 11:67-77
-
(1993)
Mol. Simul.
, vol.11
, pp. 67-77
-
-
Scully, J.L.1
Hermans, J.2
-
100
-
-
0026939543
-
Exact energy-momentum conserving algorithms and symplectic schemes for nonlinear dynamics
-
Simo JC, Tarnow N, Wang KK. 1994. Exact energy-momentum conserving algorithms and symplectic schemes for nonlinear dynamics. Comput. Meth. Appl. Mech. Eng. 100:63-116
-
(1994)
Comput. Meth. Appl. Mech. Eng.
, vol.100
, pp. 63-116
-
-
Simo, J.C.1
Tarnow, N.2
Wang, K.K.3
-
102
-
-
0000306715
-
Long time scale molecular dynamics subspace integration method applied to anharmonic crystals and glasses
-
Space B, Rabitz H, Askar A. 1993. Long time scale molecular dynamics subspace integration method applied to anharmonic crystals and glasses. J. Chem. Phys. 99:9070-79
-
(1993)
J. Chem. Phys.
, vol.99
, pp. 9070-9079
-
-
Space, B.1
Rabitz, H.2
Askar, A.3
-
103
-
-
84986534166
-
New spherical-cutoff methods for long-range forces in macromolecular simulation
-
Steinbach PJ, Brooks BR. 1994. New spherical-cutoff methods for long-range forces in macromolecular simulation. J. Comput. Chem. 15:667-83
-
(1994)
J. Comput. Chem.
, vol.15
, pp. 667-683
-
-
Steinbach, P.J.1
Brooks, B.R.2
-
105
-
-
0001144596
-
A multiple time-step method for molecular dynamics simulations of fluids of chain molecules
-
Swindoll RD, Haile JM. 1984. A multiple time-step method for molecular dynamics simulations of fluids of chain molecules. J. Chem. Phys. 53:289-98
-
(1984)
J. Chem. Phys.
, vol.53
, pp. 289-298
-
-
Swindoll, R.D.1
Haile, J.M.2
-
106
-
-
36549099461
-
Conformational equilibrium in the alanine dipeptide in the gas phase and aqueous solution: A comparison of theoretical results
-
Tobias DJ, Brooks CL III. 1988. Conformational equilibrium in the alanine dipeptide in the gas phase and aqueous solution: a comparison of theoretical results. J. Chem. Phys. 89:5115-26
-
(1988)
J. Chem. Phys.
, vol.89
, pp. 5115-5126
-
-
Tobias, D.J.1
Brooks III, C.L.2
-
107
-
-
36549101565
-
Comment on constrained molecular dynamics of macromolecules
-
Toxvaerd S. 1987. Comment on constrained molecular dynamics of macromolecules. J. Chem. Phys. 87:6140-43
-
(1987)
J. Chem. Phys.
, vol.87
, pp. 6140-6143
-
-
Toxvaerd, S.1
-
108
-
-
0000454851
-
Potential-scaled molecular dynamics and potential annealing: Effective conformational search techniques for biomolecules
-
Tsujishita H, Moriguchi I, Hirono S. 1993. Potential-scaled molecular dynamics and potential annealing: effective conformational search techniques for biomolecules. J. Phys. Chem. 97:4416-20
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 4416-4420
-
-
Tsujishita, H.1
Moriguchi, I.2
Hirono, S.3
-
109
-
-
0012515413
-
Molecular dynamics in systems with multiple time scales: Systems with stiff and soft degrees of freedom and with short and long range forces
-
Tuckerman ME, Berne BJ. 1992. Molecular dynamics in systems with multiple time scales: systems with stiff and soft degrees of freedom and with short and long range forces. J. Comput. Chem. 95:8362-64
-
(1992)
J. Comput. Chem.
, vol.95
, pp. 8362-8364
-
-
Tuckerman, M.E.1
Berne, B.J.2
-
111
-
-
84986468509
-
Reduced variable molecular dynamics
-
Turner J, Weiner P, Robson B, Venugopal R, Schubele H III, Singh R. 1995. Reduced variable molecular dynamics. J. Comput. Chem. 16:1271-90
-
(1995)
J. Comput. Chem.
, vol.16
, pp. 1271-1290
-
-
Turner, J.1
Weiner, P.2
Robson, B.3
Venugopal, R.4
Schubele III, H.5
Singh, R.6
-
112
-
-
0039953295
-
Variable reduction techniques applied to molecular dynamics simulations
-
ed. WF van Gunsteren, PK Weiner, AJ Wilkinson, Chap. 24. Leiden, The Netherlands: ESCOM
-
Turner JD, Weiner PK, Chun HM, Lupi V, Gallion S, Singh UC. 1993. Variable reduction techniques applied to molecular dynamics simulations. In Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications, ed. WF van Gunsteren, PK Weiner, AJ Wilkinson, Chap. 24. Leiden, The Netherlands: ESCOM
-
(1993)
Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications
-
-
Turner, J.D.1
Weiner, P.K.2
Chun, H.M.3
Lupi, V.4
Gallion, S.5
Singh, U.C.6
-
113
-
-
84860960789
-
Constrained dynamics of flexible molecules
-
van Gunsteren WF. 1980. Constrained dynamics of flexible molecules. Mol. Phys. 40:1015-19
-
(1980)
Mol. Phys.
, vol.40
, pp. 1015-1019
-
-
Van Gunsteren, W.F.1
-
114
-
-
0000525633
-
Effect of constraints on the dynamics of macro-molecules
-
van Gunsteren WF, Karplus M. 1982. Effect of constraints on the dynamics of macro-molecules. Macromolecules 15:1528-43
-
(1982)
Macromolecules
, vol.15
, pp. 1528-1543
-
-
Van Gunsteren, W.F.1
Karplus, M.2
-
115
-
-
22944467757
-
Computer 'experiments' on classical fluids: I. Thermodynamical properties of Lennard-Jones molecules
-
Verlet L. 1967. Computer 'experiments' on classical fluids: I. Thermodynamical properties of Lennard-Jones molecules. Phys. Rev. 159:98-103
-
(1967)
Phys. Rev.
, vol.159
, pp. 98-103
-
-
Verlet, L.1
-
117
-
-
0000240098
-
Dynamics of molecules with internal degrees of freedom by multiple time-step methods
-
Watanabe M, Karplus M. 1993. Dynamics of molecules with internal degrees of freedom by multiple time-step methods. J. Chem. Phys. 99:8063-74
-
(1993)
J. Chem. Phys.
, vol.99
, pp. 8063-8074
-
-
Watanabe, M.1
Karplus, M.2
-
118
-
-
0001183716
-
Simulations of macromolecules by multiple time-step methods
-
Watanabe M, Karplus M. 1995. Simulations of macromolecules by multiple time-step methods. J. Phys. Chem. 99:5680-97
-
(1995)
J. Phys. Chem.
, vol.99
, pp. 5680-5697
-
-
Watanabe, M.1
Karplus, M.2
-
119
-
-
4244017466
-
Symplectic maps for the n-body problem: Stability analysis
-
Wisdom J, Holman M. 1992. Symplectic maps for the n-body problem: stability analysis. Astron. J. 104:2022-29
-
(1992)
Astron. J.
, vol.104
, pp. 2022-2029
-
-
Wisdom, J.1
Holman, M.2
-
120
-
-
3843106608
-
Backward-Euler and other methods for simulating molecular fluids
-
Wu J, Watts RO. 1995. Backward-Euler and other methods for simulating molecular fluids. J. Chem. Phys. 103:3718-32
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 3718-3732
-
-
Wu, J.1
Watts, R.O.2
-
121
-
-
84913583406
-
LIN: A new algorithm combining implicit integration and normal mode techniques for molecular dynamics
-
Zhang G, Schlick T. 1993. LIN: a new algorithm combining implicit integration and normal mode techniques for molecular dynamics. J. Comput. Chem. 14:1212-33
-
(1993)
J. Comput. Chem.
, vol.14
, pp. 1212-1233
-
-
Zhang, G.1
Schlick, T.2
-
122
-
-
0001299323
-
The Langevin/implicit-Euler/Normal-Mode scheme (LIN) for molecular dynamics at large time steps
-
Zhang G, Schlick T. 1994. The Langevin/implicit-Euler/Normal-Mode scheme (LIN) for molecular dynamics at large time steps. J. Chem. Phys. 101:4995-5012
-
(1994)
J. Chem. Phys.
, vol.101
, pp. 4995-5012
-
-
Zhang, G.1
Schlick, T.2
-
123
-
-
0012579993
-
Implicit discretization schemes for Langevin dynamics
-
Zhang G, Schlick T. 1995. Implicit discretization schemes for Langevin dynamics. Mol. Phys. 84:1077-98
-
(1995)
Mol. Phys.
, vol.84
, pp. 1077-1098
-
-
Zhang, G.1
Schlick, T.2
-
124
-
-
0009077367
-
A new molecular dynamics method combining the reference system propagator algorithm with a fast multipole method for simulating proteins and other complex systems
-
Zhou R, Berne BJ. 1995. A new molecular dynamics method combining the reference system propagator algorithm with a fast multipole method for simulating proteins and other complex systems. J. Chem. Phys. 103:9444-59
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 9444-9459
-
-
Zhou, R.1
Berne, B.J.2
|