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  Molecular dynamics in principal component space.

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.

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http://pubs.acs.org/doi/pdf/10.1021/jp209964a (Publisher version)
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Michielssens, S., Author
van Erp, T. S., Author
Kutzner, C.1, Author           
Ceulemans, A., Author
de Groot, B. L.1, Author           
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1Research Group of Computational Biomolecular Dynamics, MPI for biophysical chemistry, Max Planck Society, ou_578573              

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 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.

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Language(s): eng - English
 Dates: 2012-01-202012-07-26
 Publication Status: Issued
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 Rev. Type: Peer
 Identifiers: DOI: 10.1021/jp209964a
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Title: Journal of Physical Chemistry B
Source Genre: Journal
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Pages: - Volume / Issue: 116 (29) Sequence Number: - Start / End Page: 8350 - 8357 Identifier: -