PNNL

Abstract

A series of ca. 20-ns molecular dynamics simulation runs of the N-terminal H4 histone tail in its un- and tetra-acetylated forms were performed using three different long-range electrostatic treatments namely, spherical-cutoff, reaction field and particle mesh Ewald. Comparison of the dynamical properties of the peptide reveals that internal flexibility and sampling of the conformational space are heavily dependent on the chosen method. Among the three tested methods, the particle mesh Ewald treatment yields the least conformational variation and a structural stabilization tendency around the initially defined topological framework.