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Generalized Langevin dynamics simulation: numerical integration and application of the generalized Langevin equation with an exponential model for the friction kernel

SHUN ZHOU WAN CUN XIN WANG YUN YU S

Abstract

An efficient procedure is introduced for a generalized Langevin dynamics simulation when the exponential model is taken for the friction kernel. The leap frog algorithm is used for numerical integration of the generalized Langevin equation. Simulation with this model has been performed on a cyclic undecapeptide, cyclosporin A (CPA). By comparison with the results obtained from previous simulations, the method proves to be reliable and efficient in the simulation of CPA.

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Key concepts: Langevin dynamics, Brownian dynamics, Langevin equation, Kernel (algebra), Exponential function, Statistical physics, Dynamics (music), Applied mathematics