Journal
JOURNAL OF CHEMICAL PHYSICS
Volume 118, Issue 9, Pages 4261-4271Publisher
AMER INST PHYSICS
DOI: 10.1063/1.1542611
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An efficient concerted rotation algorithm for use in Monte Carlo statistical mechanics simulations of polypeptides is reported that includes flexible bond and dihedral angles. A Gaussian bias is applied with driver bond and dihedral angles to optimize the sampling efficiency. Jacobian weighting is required in the Metropolis test to correct for imbalances in resultant transition probabilities. Testing of the methodology includes Monte Carlo simulations for polyalanines with 8-14 residues and a 36-residue protein as well as a search to find the lowest-energy conformer of the pentapeptide Met-enkephalin. The results demonstrate the formal correctness and efficiency of the method. (C) 2003 American Institute of Physics.
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