Keep It Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS - Publication - Bridge of Knowledge

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Keep It Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS

Abstract

We describe a versatile method to enforce the rotation of subsets of atoms, e.g., a protein subunit, in molecular dynamics (MD) simulations. In particular, we introduce a “flexible axis” technique that allows realistic flexible adaptions of both the rotary subunit as well as the local rotation axis during the simulation. A variety of useful rotation potentials were implemented for the GROMACS 4.5 MD package. Application to the molecular motor F1-ATP synthase demonstrates the advantages of the flexible axis approach over the established fixed axis rotation technique.

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Authors (3)

  • Photo of  Carsten Kutzner

    Carsten Kutzner

    • Max Planck Institute for Biophysical Chemistry Dept. Theoretical and Computational Biophysics
  • Photo of prof. dr hab. inż. Jacek Czub

    Jacek Czub prof. dr hab. inż.

    • Max Planck Institute for Biophysical Chemistry Dept. Theoretical and Computational Biophysics
  • Photo of  Helmut Grubmüller

    Helmut Grubmüller

    • Max Planck Institute for Biophysical Chemistry Dept. Theoretical and Computational Biophysics

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Details

Category:
Articles
Type:
artykuł w czasopiśmie wyróżnionym w JCR
Published in:
Journal of Chemical Theory and Computation no. 7, edition 5, pages 1381 - 1393,
ISSN: 1549-9618
Language:
English
Publication year:
2011
Bibliographic description:
Kutzner C., Czub J., Grubmüller H.: Keep It Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS// Journal of Chemical Theory and Computation. -Vol. 7, iss. 5 (2011), s.1381-1393
DOI:
Digital Object Identifier (open in new tab) 10.1021/ct100666v
Verified by:
Gdańsk University of Technology

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