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dc.contributor.authorZheng, Wenwei
Rohrdanz, Mary A.
Clementi, Cecilia
dc.date.accessioned 2014-12-15T20:35:08Z
dc.date.available 2014-12-15T20:35:08Z
dc.date.issued 2013
dc.identifier.citation Zheng, Wenwei, Rohrdanz, Mary A. and Clementi, Cecilia. "Rapid Exploration of Configuration Space with Diffusion-Map-Directed Molecular Dynamics." The Journal of Physical Chemistry C, 117, no. 42 (2013) American Chemical Society: 12769-12776. http://dx.doi.org/10.1021/jp401911h.
dc.identifier.urihttps://hdl.handle.net/1911/78749
dc.description.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.
dc.language.iso eng
dc.publisher American Chemical Society
dc.rights This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by the American Chemical Society.
dc.title Rapid Exploration of Configuration Space with Diffusion-Map-Directed Molecular Dynamics
dc.type Journal article
dc.contributor.funder National Science Foundation
dc.contributor.funder Welch Foundation
dc.contributor.funder National Institutes of Health
dc.citation.journalTitle The Journal of Physical Chemistry C
dc.subject.keyworddiffusion map
molecular dynamics
umbrella sampling
dc.citation.volumeNumber 117
dc.citation.issueNumber 42
dc.type.dcmi Text
dc.identifier.doihttp://dx.doi.org/10.1021/jp401911h
dc.identifier.pmcid PMC3808479
dc.identifier.pmid 23865517
dc.identifier.grantID CDI-type I grant 0835824 (National Science Foundation)
dc.identifier.grantID CHE-1152344 (National Science Foundation)
dc.identifier.grantID OCI-0959097 (National Science Foundation)
dc.identifier.grantID OCI-1053575 (National Science Foundation)
dc.identifier.grantID C-1570 (Welch Foundation)
dc.identifier.grantID NCRR S10RR02950 (National Institutes of Health)
dc.type.publication post-print
dc.citation.firstpage 12769
dc.citation.lastpage 12776


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