Molecular dynamics simulations of a cyclic-DP-240 amylose fragment in a periodic cell: Glass transition temperature and water diffusion

Molecular dynamics simulations using AMB06C, an in-house carbohydrate force field, (NPT ensembles, 1 atm) were carried out on a periodic cell that contained a cyclic 240 glucose residue amylose fragment (c-DP-240) and TIP3P water molecules. Molecular conformation and movement of the amylose fragment and water molecules at different temperatures were examined. The periodic cell volume, density, and potential energy were determined at temperatures above and below the glass transition temperature (T_g) in 25 K increments_. The amorphous cell is constructed through successive dynamic equilibration steps at temperatures above the assumed T_g value and the temperature successively lowered until several temperature points were obtained below T_g. Molecular dynamics simulations were continued for at least 500 ps or until the volume drift stopped and remained constant for several hundred picoseconds. The T_g values were found by noting the discontinuity in slope of the volume (V), potential energy (PE), or density (ρ) versus 1/T. The changes in flexibility and motion of the amylose chain as well as differences in self diffusion coefficients of water molecules are described. The final average T_g value found (316 K) is in agreement with experimental values, i.e. 320 K.