Replica-Exchange Method in van der Waals Radius Space: Overcoming Steric Restrictions for Biomolecules

TL;DR

This paper introduces a novel Hamiltonian replica-exchange method that exchanges van der Waals radii instead of temperature, enabling better sampling of biomolecular conformations by overcoming steric and energy barriers.

Contribution

The paper presents a new replica-exchange approach that modifies van der Waals radii to improve conformational sampling in biomolecular simulations.

Findings

Enhanced sampling of conformations in alanine dipeptide

Overcame steric restrictions and energy barriers

Compared favorably with conventional methods

Abstract

We present a new type of the Hamiltonian replica-exchange method, in which not temperatures but the van der Waals radius parameter is exchanged. By decreasing the van der Waals radii that control spatial sizes of atoms, this Hamiltonian replica-exchange method overcomes the steric restrictions and energy barriers. Furthermore, the simulation based on this method escapes from the local-minimum free-energy states and realizes effective sampling in the conformational space. We applied this method to an alanine dipeptide in aqueous solution and showed the effectiveness of the method by comparing the results with those obtained from the conventional canonical method.