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Discrete Molecular Dynamics (DMD)

References

Dokholyan, NV, Buldyrev, SV, Stanley, HE, and EI Shaknovich. Discrete molecular dynamics studies of the folding of a protein-like model. (1998) Folding & Design 3:577-87
Ding F, Dokholyan NV. Emergence of protein fold families through rational design. Public Library of Science Comput Biol. (2006) 2(7):e85
Yin S, Ding F, Dokholyan NV. Eris: an automated estimator of protein stability. Nat Methods. 2007 Jun;4(6):466-7.
Ab initio folding of proteins with all-atom discrete molecular dynamics. Ding F, Tsao D, Nie H, Dokholyan NV.Structure. 2008 Jul;16(7):1010-8

Background

DMD is an efficient method of computing molecular dynamic simulations. The primary efficiency that distinguishes DMD from "classical" molecular dynamics is the discretization of the potential function. Updates are done when a "collision" happens. A collision is defined as whenever the distance between a pair of centers reaches a potential step. DMD approaches classical MD in the limit as the number of potential steps increases. Simulations can be run at varying resolution from bead models to full atomic structures.

Software

Download

DMD programs are currently command line based, closed source and will be available for download soon.

Documentation

Brief overview

How to add a new residue

Caveats

Examples

ExampleOne


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Last modified 8 years ago Last modified on Dec 17, 2010 2:43:20 PM