Berlin 2005 – scientific programme

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AKB: Biologische Physik

AKB 100: Poster Session I

AKB 100.33: Poster

Saturday, March 5, 2005, 16:45–18:45, Poster TU D

Beyond Replica-Exchange: An Efficient Method for Biomolecular Simulation — •Marcus Kubitzki and Bert de Groot — Max Planck Institute for Biophysical Chemistry, Computational Biomolecular Dynamics Group, Am Fassberg 11, 37077 Göttingen

Understanding protein function requires an extensive sampling of the systems’ conformational space. In this respect, conventional molecular dynamics (MD) simulations are rather inefficient because of the currently accessible timescales of typically nanoseconds. Put differently, this sampling problem arises from the system being trapped in local-energy minima from which it can only infrequently escape at physiological temperatures.

Generalized ensemble algorithms greatly alleviate this trapping-problem. Among these methods, replica-exchange MD (REMD) has in recent years successfully been applied to a number of conformational studies of proteins. However, for simulations with full atomic resolution including explicit solvent even REMD is computationally prohibitive for many systems.

The efficiency of the REMD method is basically determined by the temperature differences between the simulated replicas. In explicit solvent simulations, these temperature steps are limited by the large number of degrees of freedom in the simulated system. Here, we systematically study ways to circumvent this problem and to achieve a highly efficient method for the conformational sampling in molecular simulations.