Multi-Overlap Simulations for Transitions between Reference Configurations

Abstract

We introduce a new procedure to construct weight factors, which flatten the probability density of the overlap with respect to some pre-defined reference configuration. This allows one to overcome free energy barriers in the overlap variable. Subsequently, we generalize the approach to deal with the overlaps with respect to two reference configurations so that transitions between them are induced. We illustrate our approach by simulations of the brainpeptide Met-enkephalin with the ECEPP/2 energy function using the global-energy-minimum and the second lowest-energy states as reference configurations. The free energy is obtained as functions of the dihedral and the root-mean-square distances from these two configurations. The latter allows one to identify the transition state and to estimate its associated free energy barrier.

12 pages, (RevTeX), 14 figures, Phys. Rev. E, submitted

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• Effective Sampling in the Configurational Space by the Multicanonical-Multioverlap Algorithm
• Shape transformations of toroidal vesicles
• Identification of Characteristic Protein Folding Channels in a Coarse-Grained Hydrophobic-Polar Peptide Model
• Structural Properties of Small Semiconductor-Binding Synthetic Peptides
• Rugged Metropolis Sampling with Simultaneous Updating of Two Dynamical Variables
• Enhanced Sampling Algorithms