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An adaptive bias – hybrid MD/kMC algorithm for protein folding and aggregation

Peter, Emanuel K. ; Shea, Joan-Emma



Abstract

In this paper, we present a novel hybrid Molecular Dynamics/kinetic Monte Carlo (MD/kMC) algorithm and apply it to protein folding and aggregation in explicit solvent. The new algorithm uses a dynamical definition of biases throughout the MD component of the simulation, normalized in relation to the unbiased forces. The algorithm guarantees sampling of the underlying ensemble in dependency of one ...

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