Coarse Grained Simulations of a Small Peptide: Effects of Finite Damping and Hydrodynamic Interactions

TL;DR

This paper introduces an improved Langevin integration scheme for coarse-grained Brownian Dynamics simulations that effectively incorporates hydrodynamic interactions and finite damping, enhancing the accuracy of peptide dynamics modeling.

Contribution

It presents an analytic integration method that relaxes the strong damping requirement in Brownian Dynamics, allowing for more realistic simulation of solvent effects in small biological molecules.

Findings

The new scheme captures short-time solvent effects more accurately.

Including hydrodynamic interactions improves peptide dynamic simulations.

Finite damping in Langevin dynamics is recommended for small biomolecules.

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.