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ZIBgridfree: efficient conformational analysis by partition-of-unity coupling

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Abstract

Obtaining a sufficient sampling of conformational space is a common problem in molecular simulation. We present the implementation of an umbrella-like adaptive sampling approach based on function-based meshless discretization of conformational space that is compatible with state of the art molecular dynamics code and that integrates an eigenvector-based clustering approach for conformational analysis and the computation of inter-conformational transition rates. The approach is applied to three example systems, namely \(n\)-pentane, alanine dipeptide, and a small synthetic host-guest system, the latter two including explicitly modeled solvent.

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Acknowledgments

We would like to thank Larissa von Krbek and Prof. Dr. Christoph Schalley for providing their host-guest system for the binding study. The work of John Hunter (1968–2012), whose creation Matplotlib is extensively used in the ZIBMolPy library, is gratefully acknowledged. Furthermore, we would like to thank the Deutsche Forschungsgemeinschaft (SFB 765) for financial support.

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Authors and Affiliations

  1. Computational Molecular Design Group, Zuse Institute Berlin, Berlin, Germany

    Alexander Bujotzek, Ole Schütt, Adam Nielsen, Konstantin Fackeldey & Marcus Weber

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  1. Alexander Bujotzek
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  2. Ole Schütt
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  3. Adam Nielsen
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  4. Konstantin Fackeldey
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  5. Marcus Weber
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Correspondence to Konstantin Fackeldey.

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Bujotzek, A., Schütt, O., Nielsen, A. et al. ZIBgridfree: efficient conformational analysis by partition-of-unity coupling. J Math Chem 52, 781–804 (2014). https://doi.org/10.1007/s10910-013-0265-1

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