Regensburg 2010 – scientific programme

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BP: Fachverband Biologische Physik

BP 5: Posters: Biopolymers and Biomaterials

BP 5.6: Poster

Monday, March 22, 2010, 17:15–20:00, Poster B1

Coarse Grained Simulations of a Small Peptide: Effects of Finite Damping and Hydrodynamic Interactions — •Tihamer Geyer — Zentrum für Bioinformatik, Universität des Saarlandes, D-66123 Saarbrücken

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 [1] 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 [2].

We also present our recently released "Brownmove" simulation package for coarse-grained many-particle simulations incorporating the above explained propagation techniques.

[1] Geyer, Winter, J. Chem. Phys., 130 (2009) 114905

[2] Winter, Geyer, J. Chem. Phys. 131 (2009) 104102