Rapid Exploration of Configuration Space with Diffusion-Map-Directed Molecular Dynamics

Simple item page
dc.citation.firstpage12769
dc.citation.issueNumber42
dc.citation.journalTitleThe Journal of Physical Chemistry C
dc.citation.lastpage12776
dc.citation.volumeNumber117
dc.contributor.authorZheng, Wenwei
dc.contributor.authorRohrdanz, Mary A.
dc.contributor.authorClementi, Cecilia
dc.date.accessioned2014-12-15T20:35:08Z
dc.date.available2014-12-15T20:35:08Z
dc.date.issued2013
dc.description.abstractThe 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.
dc.identifier.citationZheng, Wenwei, Rohrdanz, Mary A. and Clementi, Cecilia. "Rapid Exploration of Configuration Space with Diffusion-Map-Directed Molecular Dynamics." <i>The Journal of Physical Chemistry C,</i> 117, no. 42 (2013) American Chemical Society: 12769-12776. http://dx.doi.org/10.1021/jp401911h.
dc.identifier.doihttp://dx.doi.org/10.1021/jp401911h
dc.identifier.urihttps://hdl.handle.net/1911/78749
dc.language.isoeng
dc.publisherAmerican Chemical Society
dc.rightsThis is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by the American Chemical Society.
dc.subject.keyworddiffusion map
dc.subject.keywordmolecular dynamics
dc.subject.keywordumbrella sampling
dc.titleRapid Exploration of Configuration Space with Diffusion-Map-Directed Molecular Dynamics
dc.typeJournal article
dc.type.dcmiText
dc.type.publicationpost-print
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
nihms513908.pdf
Size:
2.4 MB
Format:
Adobe Portable Document Format
Description:
Download
Collections
Faculty Publications
Chemistry Publications