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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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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0027-C167-5 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0027-CF35-5
Genre: Journal Article

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2171850.pdf (Publisher version), 830KB
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http://pubs.acs.org/doi/pdf/10.1021/jp209964a (Publisher version)
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 Creators:
Michielssens, S., Author
van Erp, T. S., Author
Kutzner, C.1, Author              
Ceulemans, A., Author
de Groot, B. L.1, Author              
Affiliations:
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: Published in print
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 Rev. Method: 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: -