Abstract
Molecular dynamics simulations at atomic level have widely been used in studying macromolecular systems, such as protein, DNA and their complexes, mainly because the laws of classical statistical mechanics can largely govern the processes involved at the experimental conditions. Macromolecules, such as proteins, are characterised by dynamics with time scales ranging from nanoseconds to milliseconds. In this chapter, we discuss the molecular dynamics method as one of the most common computer simulation approach used to study molecular systems. In particular, we will present the equations of motion in the most relevant statistical ensembles used in the molecular dynamics simulations of molecular systems.
The chapter aims to introduce the classical molecular dynamics simulations of biomolecules in main statistical ensembles.
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References
M.P. Allen, D.J. Tildesley, Computer Simulation of Liquids (Oxford University Press, 1989)
H.C. Andersen, Molecular dynamics simulations at constant pressure and/or temperature. J. Chem. Phys. 72, 2384–2393 (1980)
H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, A. DiNola, J.R. Haak, Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81, 3684–3690 (1984)
B.R. Brooks, C.L. Brooks, A.D. MacKerell, L. Nilsson, R.J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A.R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R.W. Pastor, C.B. Post, J.Z. Pu, M. Schaefer, B. Tidor, R.M. Venable, H.L. Woodcock, X. Wu, W. Yang, D.M. York, M. Karplus, Charmm: the bimolecular simulation program. J. Comput. Chem. 30(10), 1545–1614 (2009)
T. Cagin, B.M. Pettitt, Molecular dynamics with a variable number of molecules. Mol. Phys. 72, 169 (1991)
T. Cagin, B.M. Pettitt, Grand molecular dynamics: a method for open systems. Mol. Simul. 6, 5 (1991)
A.W. Duster, C. Hung Wang, H. Lin, Adaptive QM/MM for molecular dynamics simulations: 5. On the energy-conserved permuted adaptive-partitioning schemes. Molecules 23, 2170 (2018)
M.J. Field, P.A. Bash, M. Karplus, A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations. J. Comput. Chem. 11, 700 (1990)
J. Gao, Potential of mean force for the isomerization of DMF in aqueous solution: a Monte Carlo QM/MM simulation study. J. Am. Chem. Soc. 115, 2930 (1993)
J. Gao, Hybrid quantum and molecular mechanical simulations an alternative avenue to solvent effects in organic chemistry. Acc. Chem. Res. 29, 298 (1996)
T.S. Hofer, S.P. de Visser, Editorial: quantum mechanical/molecular mechanical approaches for the investigation of chemical systems - recent developments and advanced applications. Front. Chem. 6, 357 (2018)
W.G. Hoover, Canonical dynamics: equilibrium phase-space distributions. Phys. Rev. A 31, 1695 (1985)
J. Ji, B.M. Pettitt, Phase transitions of water at constant excess chemical potential. An application of grand molecular dynamics. Mol. Phys. 82, 67–83 (1994)
J. Ji, T. Cagin, B.M. Pettitt, Dynamic simulations of water at constant chemical potential. J. Chem. Phys. 96, 1333 (1992)
H. Kamberaj, Molecular Dynamics Simulations In Statistical Physics: Theory And Applications Computational Series. (Springer Nature, Switzerland, 2020)
M. Karplus, J.A. McCammon, Molecular dynamics simulations of biomolecules. Nat. Struct. Biol. 9(9), 646–652 (2002). With corrigenda in Nat. Struct. Biol. 9(10), 788 (2002)
C. Lo, B.J. Palmer, Alternative Hamiltonian for molecular dynamics simulations in the grand canonical ensemble. J. Chem. Phys. 102, 925 (1995)
G.C. Lynch, B.M. Pettitt, Grand canonical ensemble molecular dynamics simulations: reformulation of extended system dynamics approaches. J. Chem. Phys. 107, 8594 (1997)
G.J. Martyna, D.J. Tobias, M.L. Klein, Constant pressure molecular dynamics algorithms. J. Chem. Phys. 101(5), 4177–4189 (1994)
G.J. Martyna, M.E. Tuckerman, D.J. Tobias, M.L. Klein, Explicit reversible integrators for extended systems dynamics. Mol. Phys. 87(5), 1117–1157 (1996)
S. Melchionna, G. Ciccotti, B.L. Holian, Hoover NPT dynamics for systems varying in shape and size. Mol. Phys. 78, 533–544 (1993)
S. Nosé, A molecular dynamics method for simulation in the canonical ensemble. Mol. Phys. 52, 255–268 (1984)
S. Nosé, A molecular dynamics method for simulation in the canonical ensemble. Mol. Phys. 52, 255 (1984)
S. Nosé, A unified formulation of the constant temperature molecular dynamics methods. J. Chem. Phys. 81, 511–519 (1984)
S. Nosé, Constant temperature molecular dynamics methods. Prog. Theor. Phys. Supp. 103, 1–46 (1991)
S. Nosé, M.L. Klein, Constant pressure molecular dynamics for molecular systems. Mol. Phys. 50, 1055–1076 (1983)
B.J. Palmer, C. Lo, Molecular dynamics implementation of the Gibbs-Ensemble calculation. J. Chem. Phys. 101, 10899–10907 (1994)
R.W. Pastor, Techniques and Applications of Langevin Dynamics Simulations In The Molecular Dynamics of Liquid Crystals. (Kluwer Academic, Dordrecht, The Netherlands, 1994)
S. Pezeshki, H. Lin, Molecular dynamics simulations of ion solvation by flexible-boundary QM/MM: on-the-fly partial charge transfer between QM and MM subsystems. J. Comp. Chem. 35, 1778–1788 (2014)
J.P. Ryckaert, G. Ciccotti, H.J.C. Berendsen, Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of \(n\)-alkanes. J. Comput. Phys. 23, 327–341 (1977)
A. Warshel, Molecular dynamics simulations of biological reactions. Acc. Chem. Res. 35, 385 (2002)
A. Warshel, M. Levitt, Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J. Mol. Biol. 103, 227–249 (1976)
S. Weerasinghe, B.M. Pettitt, Ideal chemical potential contribution in molecular dynamics simulations of the grand canonical ensemble. Mol. Phys. 82, 897 (1994)
K. Zare, V. Szebehely, Time transformations in the extended phase-space. Celest. Mech. 11, 469 (1975)
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Kamberaj, H. (2023). Classical Molecular Dynamics Simulations of Biomolecules. In: Computer Simulations in Molecular Biology. Scientific Computation. Springer, Cham. https://doi.org/10.1007/978-3-031-34839-6_5
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