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 boththe rotary subunit as well as the local rotation axis during the simulation. A variety of useful rotation potentials wereimplemented for the GROMACS 4.5 MD package. Application to the molecular motor F1-ATP synthase demonstrates the advantages ofthe flexible axis approach over the established fixed axis rotation technique.
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