Exploring biomolecular dynamics and interactions using advanced sampling methods

Manuel Luitz, Rainer Bomblies, Katja Ostermeir, Martin Zacharias

Research output: Contribution to journalReview articlepeer-review

26 Scopus citations

Abstract

Molecular dynamics (MD) and Monte Carlo (MC) simulations have emerged as a valuable tool to investigate statistical mechanics and kinetics of biomolecules and synthetic soft matter materials. However, major limitations for routine applications are due to the accuracy of the molecular mechanics force field and due to the maximum simulation time that can be achieved in current simulations studies. For improving the sampling a number of advanced sampling approaches have been designed in recent years. In particular, variants of the parallel tempering replica-exchange methodology are widely used in many simulation studies. Recent methodological advancements and a discussion of specific aims and advantages are given. This includes improved free energy simulation approaches and conformational search applications.

Original languageEnglish
Article number323101
JournalJournal of Physics Condensed Matter
Volume27
Issue number32
DOIs
StatePublished - 19 Aug 2015
Externally publishedYes

Keywords

  • accelerated sampling
  • conformational sampling
  • force field calculation
  • molecular dynamics simulations
  • peptide and protein folding
  • potential scaling

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