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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)
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Carsten Kutzner
- Max Planck Institute for Biophysical Chemistry Dept. Theoretical and Computational Biophysics
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Jacek Czub prof. dr hab. inż.
- Max Planck Institute for Biophysical Chemistry Dept. Theoretical and Computational Biophysics
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Helmut Grubmüller
- Max Planck Institute for Biophysical Chemistry Dept. Theoretical and Computational Biophysics
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- Accepted or Published Version
- DOI:
- Digital Object Identifier (open in new tab) 10.1021/ct100666v
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- Category:
- Articles
- Type:
- artykuł w czasopiśmie wyróżnionym w JCR
- Published in:
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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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