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.
Authors
- Carsten Kutzner,
- prof. dr hab. inż. Jacek Czub link open in new tab ,
- Helmut Grubmüller
Additional information
- DOI
- Digital Object Identifier link open in new tab 10.1021/ct100666v
- Category
- Publikacja w czasopiśmie
- Type
- artykuł w czasopiśmie wyróżnionym w JCR
- Language
- angielski
- Publication year
- 2011
