title: 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 F(1)-ATP synthase demonstrates the advantages of the flexible axis approach over the established fixed axis rotation technique.
authors.affiliation: Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
authors.forename: Carsten
authors.initials: C
authors.lastname: Kutzner
authors.forename: Jacek
authors.initials: J
authors.lastname: Czub
authors.forename: Helmut
authors.initials: H
authors.lastname: Grubmüller