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

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

2009-11-05

arxiv.org/abs/0911.1011v1

Physics

Condensed Matter

Statistical Mechanics

14 pages, (Revtex4), 11 figures

Scientific paper

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.

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