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.

Original languageEnglish (US)
Pages (from-to)80-92
Number of pages13
JournalWiley Interdisciplinary Reviews: Computational Molecular Science
Volume1
Issue number1
DOIs
StatePublished - Jan 1 2011

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Computational Mathematics
  • Materials Chemistry

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