Paper Citing NAMD - Abstract
Chen, Cong; Li, Wei Zhong; Song, Yong Chen; Yang, Jian
Hydrogen bonding analysis of glycerol aqueous solutions: A molecular dynamics simulation study
JOURNAL OF MOLECULAR LIQUIDS, 146:23-28, MAY 31 2009
Glycerol-water systems with different concentrations have been simulated using a molecular dynamics simulation method. The study is the beginning of the project to research intracellular ice formation with micro-scale simulation methods. The H center dot center dot center dot O distance and H-O center dot center dot center dot O angle have been selected as the geometry criteria for hydrogen bonding analysis. The percentages of atoms and molecules with different number of hydrogen bonds and the mean numbers of hydrogen bonds per atom and per molecule have been studied. It has been found that the hydrogen bonding ability of oxygen atom in water is stronger than that of oxygen atoms in glycerol and the hydrogen bonding ability of hydrogen atoms in water is weaker than that of hydrogen atoms in glycerol. As glycerol concentration increases, the hydrogen bonding ability of oxygen atom in water slightly decreases and the hydrogen bonding ability of hydrogen atoms doesn't change, leading to a decrease of hydrogen bonding ability of water. The ratios of the number of acceptor atoms to the number of donor atoms for water and glycerol have been calculated and they both show a linear relation with glycerol mole fraction. To account for the hydrogen bonding dynamics. lifetimes have been reported. (C) 2009 Elsevier B.V. All rights reserved.
