Repozytorium publikacji - Politechnika Gdańska

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.

Autorzy

• Carsten Kutzner,
• prof. dr hab. inż. Jacek Czub link otwiera się w nowej karcie ,
• Helmut Grubmüller