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J Chem Theory Comput. 2013 Mar 12;9(3):1521-32. doi: 10.1021/ct3010563. Epub 2013 Feb 22.

Demonstrating the Transferability and the Descriptive Power of Sketch-Map.

Author information

1
Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom.
2
Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich and Facoltà di Informatica, Instituto di Scienza Computationali, Università della Svizzera Italiana , Via Giuseppe Buffi 13, CH-6900, Lugano, Switzerland.

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.

PMID:
26587614
DOI:
10.1021/ct3010563

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