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  g_permute: Permutation-reduced phase space density compaction.

Reinhard, F., Lange, O., Hub, J., Haas, J., & Grubmüller, H. (2009). g_permute: Permutation-reduced phase space density compaction. Computer Physics Communications, 180(3), 455-458. doi:10.1016/j.cpc.2008.10.018.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0027-C073-2 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0027-CF2F-4
Genre: Journal Article

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Reinhard, F., Author
Lange, O.F.1, Author              
Hub, J.S., Author
Haas, J.1, Author              
Grubmüller, H.1, Author              
Affiliations:
1Department of Theoretical and Computational Biophysics, MPI for biophysical chemistry, Max Planck Society, ou_578631              

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Free keywords: Permutation reduction; Solvent entropy; All-atom (fully atomistic) molecular dynamics simulations; GROMACS; Compacted configuration space density
 Abstract: Biomolecular processes are governed by free energy changes and thus depend on a fine-tuned interplay between entropy and enthalpy. To calculate accurate values for entropies from simulations is particularly challenging for the solvation shell of proteins, which contributes crucially to the total entropy of solvated proteins, due to the diffusive motion of the solvent molecules. Accordingly, for each frame of a Molecular dynamics (MD) trajectory, our software relabels the solvent molecules, such that the resulting configuration space volume is reduced by a factor of N! with N being the number of solvent molecules. The combinatorial explosion of a naive implementation is here overcome by transforming the task into a linear assignment problem, for which algorithms with complexity O(N3)O(N3) exist. We have shown in previous research that the solvent entropy can be estimated from such a compacted trajectory by established entropy estimation methods. In this paper, we describe the software implementation which also allows applications beyond entropy estimation, such as the permutation of lipids in membrane bilayers.

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Language(s): eng - English
 Dates: 2008-11-082009-03
 Publication Status: Published in print
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 Rev. Method: Peer
 Identifiers: DOI: 10.1016/j.cpc.2008.10.018
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Title: Computer Physics Communications
Source Genre: Journal
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Pages: - Volume / Issue: 180 (3) Sequence Number: - Start / End Page: 455 - 458 Identifier: -