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Well-Tempered Metadynamics as a Tool for Characterizing Multi-Component, Crystalline Molecular Machines

Ilott, Andrew J.; Palucha, Sebastian; Hodgkinson, Paul; Wilson, Mark R.

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Andrew J. Ilott

Sebastian Palucha


The well-tempered, smoothly converging form of the metadynamics algorithm has been implemented in classical molecular dynamics simulations and used to obtain an estimate of the free energy surface explored by the molecular rotations in the plastic crystal, octafluoronaphthalene. The biased simulations explore the full energy surface extremely efficiently, more than 4 orders of magnitude faster than unbiased molecular dynamics runs. The metadynamics collective variables used have also been expanded to include the simultaneous orientations of three neighboring octafluoronaphthalene molecules. Analysis of the resultant three-dimensional free energy surface, which is sampled to a very high degree despite its significant complexity, demonstrates that there are strong correlations between the molecular orientations. Although this correlated motion is of limited applicability in terms of exploiting dynamical motion in octafluoronaphthalene, the approach used is extremely well suited to the investigation of the function of crystalline molecular machines.

Journal Article Type Article
Publication Date Oct 10, 2013
Deposit Date Jun 10, 2014
Publicly Available Date Jul 18, 2014
Journal Journal of Physical Chemistry B (Soft Condensed Matter and Biophysical Chemistry)
Print ISSN 1520-6106
Electronic ISSN 1520-5207
Publisher American Chemical Society
Peer Reviewed Peer Reviewed
Volume 117
Issue 40
Pages 12286-12295
Public URL


Accepted Journal Article (2.3 Mb)

Copyright Statement
This document is the Accepted Manuscript version of a Published Work that appeared in final form in the Journal of Physical Chemistry, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see

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