Coarse grained simulations of a small peptide: Effects of finite dampingand hydrodynamic interactions

摘要

In the coarse grained Brownian dynamics (BD) simulation method the many solvent molecules arereplaced by random thermal kicks and an effective friction acting on the particles of interest. For BDthe friction has to be so strong that the particles' velocities are damped much faster than the durationof an integration timestep. Here we show that this conceptual limit can be dropped with an analyticintegration of the equations of damped motion. In the resulting Langevin integration scheme ourrecently proposed approximate form of the hydrodynamic interactions between the particles can beincorporated conveniently, leading to a fast multiparticle propagation scheme, which captures moreof the short-time and short-range solvent effects than standard BD. Comparing the dynamics of abead-spring model of a short peptide, we recommend to run simulations of small biologicalmolecules with the Langevin type finite damping and to include the hydrodynamic interactions.