Efficient parallel decomposition of dynamical sampling in glass-forming materials based on an ""on the fly"" definition of metabasins

Tsalikis, DG; Lempesis, N; Boulougouris, GC; Theodorou, DN

dc.contributor.author	Tsalikis, DG	en
dc.contributor.author	Lempesis, N	en
dc.contributor.author	Boulougouris, GC	en
dc.contributor.author	Theodorou, DN	en
dc.date.accessioned	2014-03-01T01:33:20Z
dc.date.available	2014-03-01T01:33:20Z
dc.date.issued	2010	en
dc.identifier.issn	1549-9618	en
dc.identifier.uri	https://dspace.lib.ntua.gr/xmlui/handle/123456789/20384
dc.subject	On The Fly	en
dc.subject.classification	Chemistry, Multidisciplinary	en
dc.subject.other	PROTEIN-FOLDING KINETICS	en
dc.subject.other	LENNARD-JONES MIXTURE	en
dc.subject.other	MODE-COUPLING THEORY	en
dc.subject.other	MOLECULAR-DYNAMICS	en
dc.subject.other	SUPERCOOLED LIQUIDS	en
dc.subject.other	INHERENT STRUCTURES	en
dc.subject.other	MONTE-CARLO	en
dc.subject.other	POTENTIAL SURFACES	en
dc.subject.other	INFREQUENT EVENTS	en
dc.subject.other	BROWNIAN DYNAMICS	en
dc.title	Efficient parallel decomposition of dynamical sampling in glass-forming materials based on an ""on the fly"" definition of metabasins	en
heal.type	journalArticle	en
heal.identifier.primary	10.1021/ct9004245	en
heal.identifier.secondary	http://dx.doi.org/10.1021/ct9004245	en
heal.language	English	en
heal.publicationDate	2010	en
heal.abstract	In this work, we propose a highly parallelizable sampling scheme designed for atomistic simulations of glassy materials in the vicinity of the glass-transition temperature Tg, based on the idea of inherent structures (IS). Glassy dynamics is envisioned as a combination of two types of motions: (a) an ""in basin"" vibrational motion in the vicinity of a potential energy minimum (IS), and (b) transitions from one basin to another. In order to perform efficient dynamical sampling in the vicinity of Tg, we propose an ""on the fly"" definition of metabasins (i.e., collections of basins communicating via fast transitions in which the system spends a sufficient time before moving on to a neighboring collection). Our criterion for defining metabasins is based on the rate of identification of new basins in the course of a canonical molecular dynamics (MD) run. In order to compute individual rate constants between basins and metabasins, we propose to follow a swarm of microcanonical MD trajectories initiated at phase-space points sampled by a canonical MD run that is artificially trapped within a metabasin. The execution time required by this highly parallelizable scheme is reduced dramatically, since no information exchange takes place between the microcanonical trajectories. Results from our parallel methodology are compared against results from artificially trapped canonical MD runs, in terms of the evaluated rate constants, and found to be in very good agreement. Parallel simulations have been conducted on up to 250 processors, achieving almost linear scaling. The validity of our definition of metabasins is confirmed by analysis of the resulting network of basins. © 2010 American Chemical Society.	en
heal.publisher	AMER CHEMICAL SOC	en
heal.journalName	Journal of Chemical Theory and Computation	en
dc.identifier.doi	10.1021/ct9004245	en
dc.identifier.isi	ISI:000276558100029	en
dc.identifier.volume	6	en
dc.identifier.issue	4	en
dc.identifier.spage	1307	en
dc.identifier.epage	1322	en