Rapid exploration of configuration space with diffusion-map-directed molecular dynamics

Wenwei Zheng, Mary A. Rohrdanz, Cecilia Clementi

Research output: Contribution to journalArticle

44 Citations (Scopus)

Abstract

The gap between the time scale of interesting behavior in macromolecular systems and that which our computational resources can afford often limits molecular dynamics (MD) from understanding experimental results and predicting what is inaccessible in experiments. In this paper, we introduce a new sampling scheme, named diffusion-map-directed MD (DM-d-MD), to rapidly explore molecular configuration space. The method uses a diffusion map to guide MD on the fly. DM-d-MD can be combined with other methods to reconstruct the equilibrium free energy, and here, we used umbrella sampling as an example. We present results from two systems: alanine dipeptide and alanine-12. In both systems, we gain tremendous speedup with respect to standard MD both in exploring the configuration space and reconstructing the equilibrium distribution. In particular, we obtain 3 orders of magnitude of speedup over standard MD in the exploration of the configurational space of alanine-12 at 300 K with DM-d-MD. The method is reaction coordinate free and minimally dependent on a priori knowledge of the system. We expect wide applications of DM-d-MD to other macromolecular systems in which equilibrium sampling is not affordable by standard MD.

Original languageEnglish (US)
Pages (from-to)12769-12776
Number of pages8
JournalJournal of Physical Chemistry B
Volume117
Issue number42
DOIs
StatePublished - Nov 4 2013
Externally publishedYes

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Space Flight
Molecular Dynamics Simulation
Molecular dynamics
molecular dynamics
configurations
alanine
Alanine
sampling
Sampling
Molecular Conformation
Dipeptides
Diptera
Free energy
resources
free energy

ASJC Scopus subject areas

  • Surfaces, Coatings and Films
  • Physical and Theoretical Chemistry
  • Materials Chemistry

Cite this

Rapid exploration of configuration space with diffusion-map-directed molecular dynamics. / Zheng, Wenwei; Rohrdanz, Mary A.; Clementi, Cecilia.

In: Journal of Physical Chemistry B, Vol. 117, No. 42, 04.11.2013, p. 12769-12776.

Research output: Contribution to journalArticle

Zheng, Wenwei ; Rohrdanz, Mary A. ; Clementi, Cecilia. / Rapid exploration of configuration space with diffusion-map-directed molecular dynamics. In: Journal of Physical Chemistry B. 2013 ; Vol. 117, No. 42. pp. 12769-12776.
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