PMID: 11909112Mar 23, 2002Paper

Convergence of sampling in protein simulations

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
Berk Hess

Abstract

With molecular dynamics protein dynamics can be simulated in atomic detail. Current computers are not fast enough to probe all available conformations, but fluctuations around one conformation can be sampled to a reasonable extent. The motions with the largest fluctuations can be filtered out of a simulation using covariance or principal component analysis. A problem with this analysis is that random diffusion can appear as correlated motion. An analysis is presented of how long a simulation should be to obtain relevant results for global motions. The analysis reveals that the cosine content of the principal components is a good indicator for bad sampling.

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Citations

Mar 2, 2011·Journal of Molecular Modeling·Aleksandra MiszkielSławomir Milewski
Sep 29, 2011·Journal of Molecular Modeling·Naser AlijabbariBoris Gelmont
Sep 11, 2012·Journal of Molecular Modeling·Antje Wolf, Karl N Kirschner
Sep 28, 2006·Journal of the American Chemical Society·Nathalie BasdevantMarco Ceruso
Oct 16, 2007·The Journal of Physical Chemistry. B·Edward Lyman, Daniel M Zuckerman
Nov 17, 2007·The Journal of Physical Chemistry. B·Jun FengB Montgomery Pettitt
Jun 25, 2009·The Journal of Physical Chemistry. B·Jun FengB Montgomery Pettitt
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Apr 5, 2014·The Journal of Chemical Physics·Ryuhei HaradaYasuteru Shigeta
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Feb 19, 2009·Journal of Molecular Graphics & Modelling·Sangeeta Kundu, Debjani Roy
Oct 28, 2008·Journal of Molecular Biology·Gia G MaisuradzeHarold A Scheraga
Jul 16, 2008·Journal of Molecular Graphics & Modelling·Won-Joon SonSeokmin Shin

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