Demonstrating the Transferability and the Descriptive Power of Sketch-Map

Michele Ceriotti, Gareth A. Tribello, Michele Parrinello

Research output: Contribution to journalArticle

67 Citations (Scopus)
261 Downloads (Pure)

Abstract

Increasingly, it is recognized that new automated forms of analysis are required to understand the high-dimensional output obtained from atomistic simulations. Recently, we introduced a new dimensionality reduction algorithm, sketch-map, that was designed specifically to work with data from molecular dynamics trajectories. In what follows, we provide more details on how this algorithm works and on how to set its parameters. We also test it on two well-studied Lennard-Jones clusters and show that the coordinates we extract using this algorithm are extremely robust. In particular, we demonstrate that the coordinates constructed for one particular Lennard-Jones cluster can be used to describe the configurations adopted by a second, different cluster and even to tell apart different phases of bulk Lennard-Jonesium.

Original languageEnglish
Pages (from-to)1521-1532
Number of pages12
JournalJournal of chemical theory and computation
Volume9
Issue number3
Early online date04 Feb 2013
DOIs
Publication statusPublished - 12 Mar 2013

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