Molecular dynamics in principal component space.

Michielssens, S.; van Erp, T. S.; Kutzner, C.; Ceulemans, A.; de Groot, B. L.

doi:10.1021/jp209964a

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Journal Article

Molecular dynamics in principal component space.

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Kutzner, C.
Research Group of Computational Biomolecular Dynamics, MPI for biophysical chemistry, Max Planck Society;

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de Groot, B. L.
Research Group of Computational Biomolecular Dynamics, MPI for biophysical chemistry, Max Planck Society;

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http://pubs.acs.org/doi/pdf/10.1021/jp209964a
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Citation

Michielssens, S., van Erp, T. S., Kutzner, C., Ceulemans, A., & de Groot, B. L. (2012). Molecular dynamics in principal component space. Journal of Physical Chemistry B, 116(29), 8350-8357. doi:10.1021/jp209964a.

Cite as: https://hdl.handle.net/11858/00-001M-0000-0027-C167-5

Abstract

A molecular dynamics algorithm in principal component space is presented. It is demonstrated that sampling can be improved without changing the ensemble by assigning masses to the principal components proportional to the inverse square root of the eigenvalues. The setup of the simulation requires no prior knowledge of the system; a short initial MD simulation to extract the eigenvectors and eigenvalues suffices. Independent measures indicated a 6–7 times faster sampling compared to a regular molecular dynamics simulation.