Paper Citing NAMD - Abstract
Kutzner, Carsten; Czub, Jacek; Grubmueller, Helmut
Keep It Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1381-1393, MAY 2011
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.
