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Abstract: In molecular dynamics the highly oscillatory vibrations in the chemical bonds are often replaced by holonomic constraints that freeze the bond length/angle to its equilibrium value. In some cases this approach can be justified if the force constants of the bond vibrations are sufficiently large. However, for moderate values of the force constant, the constrained system might lead to a dynamical behavior that is too "rigid" compared to the flexible model. To compensate for this effect, the... (Update)
Active bibliography (related documents): More All
0.7: Smoothed Langevin dynamics of highly oscillatory systems - Reich (1996) (Correct)
0.6: Enhanced long-term simulation of Hamiltonian systems containing a.. - Reich (1995) (Correct)
0.3: A Free Energy Approach to the Torsion Dynamics of Macromolecules - Reich (1995) (Correct)
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0.2: Symplectic Integrators for Systems of Rigid Bodies - Reich (1996) (Correct)
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BibTeX entry: (Update)
@article{ reich98modified,
author = "Sebastian Reich",
title = "Modified potential energy functions for constrained molecular dynamics",
journal = "Numerical Algorithms",
volume = "19",
number = "1--4",
pages = "213--221",
year = "1998",
url = "citeseer.ist.psu.edu/reich97modified.html" }
Citations (may not include all citations):306 Computer Simulations of Liquids (context) - Allen, Tildesley - 1987
120 CHARMM: A Program for Macromolecular Energy (context) - Brooks, Bruccoleri et al. - 1983
43 the Hamiltonian Interpolation of Near to the Identity Symple.. (context) - Benettin, Giorgilli - 1994
28 Symplectic Numerical Integrators in Constrained Hamiltonian .. - Leimkuhler, Skeel - 1994
22 Motion Under a Strong Constraining Force (context) - Rubin, Ungar - 1957
20 Generalized Verlet Algorithm for Efficient Molecular Dynamic.. (context) - Grubmuller, Heller et al. - 1991
20 Dangers of Multiple-Time-Step Methods (context) - Biesiadecki, Skeel - 1993
19 Thermodynamical Properties of Lennard-Jones Molecules (context) - Verlet, Computer - 1967
15 Smoothed Dynamics of Highly Oscillatory Hamiltonian Systems - Reich - 1995
9 Difficulties with Multiple Timestepping and the Fast Multipo.. (context) - Bishop, Skeel et al. - 1996
9 and Exponentially Small Estimates (context) - Reich - 1997
9 Realization of Holonomic Constraints and Freezing of High Fr.. (context) - Benettin, Galgani et al. - 1989
8 Elastic Molecular Dynamics with flexible Constraints (context) - Brooks, Zhou et al. - 1997
7 Rigid Constraints in Statistical Mechanics (context) - Helfand - 1979
3 Torsion Dynamics of Molecular Systems - Reich - 1996
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