Replica-Exchange Method in van der Waals Radius Space: Overcoming Steric Restrictions for Biomolecules
arXiv:0911.1011 · doi:10.1063/1.3372767
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.
14 pages, (Revtex4), 11 figures
References in corpus (6)
- Exchange Monte Carlo Method and Application to Spin Glass Simulations
- Multicanonical Ensemble: A New Approach to Simulate First-order Phase Transitions
- Multidimensional replica-exchange method for free-energy calculations
- Monte Carlo Simulations in Multibaric-Multithermal Ensemble
- Multi-Overlap Simulations for Transitions between Reference Configurations
- Effective Sampling in the Configurational Space by the Multicanonical-Multioverlap Algorithm