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Abstract
In the coarse grained Brownian Dynamics simulation method the many solvent molecules
are replaced by random thermal kicks and an effective friction acting on the particles
of interest. For Brownian Dynamics the friction has to be so strong that the particles'
velocities are damped much faster than the duration of an integration timestep. Here
we show that this conceptual limit can be dropped with an analytic integration of
the equations of damped motion. In the resulting Langevin integration scheme our recently
proposed approximate form of the hydrodynamic interactions between the particles can
be incorparated conveniently, leading to a fast multi-particle propagation scheme,
which captures more of the short-time and short-range solvent effects than standard
BD. Comparing the dynamics of a bead-spring model of a short peptide, we recommend
to run simulations of small biological molecules with the Langevin type finite damping
and to include the hydrodynamic interactions.