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WIREs Comput Mol Sci
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Discrete molecular dynamics

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Abstract Discrete molecular dynamics (DMD) has emerged as a simplification of traditional molecular dynamics (MD). DMD employs discrete step function potentials in place of the continuous potential used in traditional MD. As a result, the simulation engine solves the ballistic equations of motion for only those particles participating in a collision, instead of solving Newton's equations of motion for every particle in the system. Because fewer calculations are performed per time step, the DMD technique allows for longer time and length scales to become accessible in the simulation of large biomolecules. The use of coarse‐grained models extends the computational advantage of this method. Although some accuracy is sacrificed to speed, because of the usefulness of DMD to the simulation of many particles at longer timescales, the technique has seen application to diverse molecular systems. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 80–92 DOI: 10.1002/wcms.4 This article is categorized under: Structure and Mechanism > Molecular Structures Structure and Mechanism > Computational Biochemistry and Biophysics Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods

Discrete molecular dynamics (DMD) potentials. Schematics of the various step function potentials used in DMD. (a) Hard‐sphere interaction potential, characterized by infinite repulsion at the hard‐sphere radius, attractive potential well, and zero interaction after a given radius. (b) Single‐infinite square well used for covalent bonds, angular constraints, and base‐stacking interactions. (c) Dihedral constraint potential. (d) Hydrogen‐bonding auxiliary distance potential function. (e) Discretized van der Waals and solvation nonbonded interactions potential. (f) Base‐pairing interaction potential. (g) Lysine–arginine‐phosphate interaction potential in DNA–histone nucleosome complex.

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Coarse‐grained models for biomacromolecules. (a) RNA and DNA three‐bead model. Black circles represent beads, thick solid lines represent covalent bonds, dashed lines represent angular constraints, thin dotted lines represent dihedral constraints, thin solid lines represent base‐stacking interactions, and thick dotted lines represent base‐pairing interactions. (b) Lipid three‐bead model. Black beads represent fatty acid chains, whereas gray bead represents both head group and glycerol backbone. All beads have a radius of σ.

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Coarse‐grained protein models. Schematics for coarse‐grained models of varied resolution used for proteins in discrete molecular dynamics simulations. Circles represent beads or atoms, with gray circles being optional beads that may or may not be used for all amino acids. Thick, solid lines represent covalent bonds, whereas thin dashed lines represent angular constraints. Elliptical arrows represent dihedral constraints. (a) Two‐bead protein model. (b) Four‐bead protein model. (c) Hydrogen bonding with the reaction algorithm; thick dashed line represents the hydrogen bond. (d) All‐atom protein model. (e) Quasi‐all‐atom protein model.

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Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods
Structure and Mechanism > Molecular Structures
Structure and Mechanism > Computational Biochemistry and Biophysics

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