Abstract
An efficient sampling method for protein structure using molecular dynamics (MD) simulation and a three-dimensional reference interaction-site model (3D-RISM) theory has been developed based on the hybrid Monte Carlo framework. In this method, new structures are generated by MD simulation with the generalized Born implicit solvent model and the Metropolis-like criterion to accept or reject the structure candidate is applied based on the free energy corresponding to the 3D-RISM Hamiltonian at each specified time propagation interval. The resulting ensemble of structures satisfies the 3D-RISM Hamiltonian-based equilibrium distribution. The method was applied to alanine dipeptide and methionine-enkephalin polypeptides in aqueous solution as test cases. The results demonstrated the efficiency of the method.
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