Journal
JOURNAL OF CHEMICAL PHYSICS
Volume 132, Issue 13, Pages -Publisher
AMER INST PHYSICS
DOI: 10.1063/1.3372767
Keywords
free energy; macromolecules; molecular biophysics; molecular configurations; proteins; sampling methods; van der Waals forces
Funding
- Grants-in-Aid for Scientific Research on Innovative Areas
- Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan
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We present a new type of the Hamiltonian replica-exchange method, where the van der Waals radius parameter and not the temperature is exchanged. By decreasing the van der Waals radii, which 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 and replica-exchange methods.
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