Albany 2001

category image Biomolecular
SUNY at Albany
June 19-23, 2001

A Multiple Copy Simulated Annealing Algorithm for Polypeptide Structure Prediction On A Beowulf PC Cluster.

In this work we describe the conformational optimization method based on multiple copy simulated annealing in torsional space and modified Generalized Born Approximation. Pair wise approximation GBA and analytical calculation of solvent accessible area are modified to include force field atom types consistent with new AMBER 5.0 force field. The multiple copy simulated annealing in torsional space algorithm is devised for molecular conformational optimization. A primary test on several short peptides are carried out. The implementation of this algorithm using MPI(Message Passing Interface) on a BEOWULF PC cluster shows a linear scale for parallelization

Yongxing Liu and David L. Beveridge

Chemistry Department and Molecular Biophysics Program Wesleyan University Middletown, CT 06457 USA
e-mail: yliu@wesleyan.edu Tel: 860-685-2777