期刊
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
卷 7, 期 5, 页码 1381-1393出版社
AMER CHEMICAL SOC
DOI: 10.1021/ct100666v
关键词
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资金
- EU [NANOMOT/NEST 029084]
- Deutsche Forschungsgemeinschaft (DFG) [GR 1590/2-1]
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.
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