Paper Citing NAMD - Abstract
Cai Kai-Cong; Wang Jian-Ping
Molecular Dynamical Structures of Glycolaldehyde
ACTA PHYSICO-CHIMICA SINICA, 25:677-683, APR 2009
From quantum chemical computations, two sets of molecular mechanics force fields based on peptides and aldehydes were developed for the simplest sugar-glycolaldehyde. Molecular dynamics simulations demonstrated that the structure of glycolaldehyde and the solvent water distribution can be better described by aldehyde-like parameters. Probabilities of normal mode frequencies and dipole derivatives were obtained by instantaneous normal mode analysis. This is thus a new way to predict the parameters of femtosecond broadband two-dimensional infrared spectroscopy for biomolecules by combining quantum mechanics calculation and molecular dynamics simulation.
