Ontology highlight
ABSTRACT:
SUBMITTER: Kutzner C
PROVIDER: S-EPMC3091370 | biostudies-literature | 2011 May
REPOSITORIES: biostudies-literature
Kutzner Carsten C Czub Jacek J Grubmüller Helmut H
Journal of chemical theory and computation 20110331 5
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 ...[more]