Paper Citing NAMD - Abstract
Chen Cong; Li Wei-Zhong
Molecular Dynamics Simulation of Hydrogen Bonding Characteristics in Aqueous Glycerol Solutions
ACTA PHYSICO-CHIMICA SINICA, 25:507-512, MAR 2009
To study the structure and physicochemical characteristics of cryoprotective agent (CPA) solutions, glycerol has been chosen as a CPA and the molecular dynamics method was used to simulate glycerol and water binary systems with different concentrations. Molecular dynamics trajectories of aqueous glycerol solutions within 2 ns were obtained. After a detailed analysis of trajectories within the last 1 ns, the intermolecular radial distribution functions for C-C, C-O, C-H, O-H, O-O and H-H pairs and the backbone conformation distributions of glycerol molecules were calculated. Based on geometrical criteria, structural and dynamics characteristics of the hydrogen bonding network were analyzed. Distribution percentages and average values of the number of hydrogen bonds per atom (O and H atoms) and per molecule (glycerol and water molecules) were calculated. The lifetimes of total hydrogen bonds, hydrogen bonds between water molecules and hydrogen bonds between glycerol and water molecules were also studied.
