Well-Tempered Metadynamics as a Tool for Characterizing Multi-Component, Crystalline Molecular Machines
نویسندگان
چکیده
منابع مشابه
Well-tempered metadynamics as a tool for characterizing multi-component, crystalline molecular machines.
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 ...
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We present a method for determining the free-energy dependence on a selected number of collective variables using an adaptive bias. The formalism provides a unified description which has metadynamics and canonical sampling as limiting cases. Convergence and errors can be rigorously and easily controlled. The parameters of the simulation can be tuned so as to focus the computational effort only ...
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Well-Tempered Metadynamics (WTmetaD) is an efficient method to enhance the reconstruction of the free-energy surface of proteins. WTmetaD guarantees a faster convergence in the long time limit in comparison with the standard metadynamics. It still suffers, however, from the same limitation, i.e., the non-trivial choice of pertinent collective variables (CVs). To circumvent this problem, we coup...
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ژورنال
عنوان ژورنال: The Journal of Physical Chemistry B
سال: 2013
ISSN: 1520-6106,1520-5207
DOI: 10.1021/jp4045995