Evaluation of efficiency of reference potential spatial warping algorithm in conformational sampling of peptides.
Molecular dynamics (MD) simulation using the reference potential spatial warping algorithm (REPSWA) is a promising method for computing the conformational equilibrium of a system with a rugged energy surface. Its effectiveness has previously been demonstrated using only a simplified model system of a hydrocarbon chain omitting nonbonded interaction terms from the potential energy function. To evaluate the applicability of REPSWA MD simulation to more realistic problems, we applied it to small peptide systems in an aqueous environment. Difficulties were encountered, however, forcing us to devise several modifications. We investigated their effectiveness in comparison to conventional constant-temperature and multicanonical MD simulations. We found that the sampling efficiency of the modified REPSWA MD after a careful optimization of its parameters was better than that of the constant-temperature MD and comparable to that of the multicanonical MD in several cases.
Ishitani
Ryuichiro
R
Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
Shimizu
Kentaro
K
Terada
Tohru
T
D000409:Alanine / Q000737:chemistry*; D000465:Algorithms; D001703:Biophysics / Q000379:methods; D002627:Chemistry, Physical / Q000379:methods*; D003198:Computer Simulation; D003201:Computers; D004744:Enkephalin, Methionine / Q000737:chemistry*; D006838:Hydrocarbons / Q000737:chemistry; D015233:Models, Statistical; D008962:Models, Theoretical; D008968:Molecular Conformation; D010455:Peptides / Q000737:chemistry*; D015203:Reproducibility of Results; D012984:Software; D013997:Time Factors
D006838:Hydrocarbons; D010455:Peptides; D004744:Enkephalin, Methionine; D000409:Alanine