Comparisons of force fields for proteins by generalized-ensemble simulations

Abstract

Secondary structural characteristics of six commonly used force fields for protein systems developed by different research groups have been compared. We performed molecular dynamics simulations of an α-helical polypeptide and a β-hairpin polypeptide with explicit water molecules. Two generalized-ensemble algorithms, replica-exchange multicanonical algorithm and multicanonical replica-exchange method, for efficient sampling of configurational space have been employed. Comparisons of the secondary structure content of polypeptides for different force fields highlighted differences of their structural tendency. The results imply that α-helix is favored for AMBER94 and AMBER99 and that β-hairpin is favored for GROMOS96, while CHARMM22, AMBER96, and OPLS-AA/L have intermediate tendency.