title: Geometry and Excitation Energy Fluctuations of NMA in Aqueous Solution with CHARMM, AMBER, OPLS, and GROMOS Force Fields: Implications for Protein Ultraviolet Spectra Simulation.
abstract: Molecular dynamics (MD) simulations are performed for N-methylamide (NMA) in water at 300 K with different force fields. Compared to the three all-atom force fields (CHARMM22, AMBER03, and OPLS-AA), the united-atom force field (GROMOS96) predicts a broader distribution of the peptide OCNH dehedral angle. A map constructed by fitting the npi* and pipi* transition energies as quadratic functions of the NMA geometric variables is used to simulate the excitation energy fluctuations. GROMOS96 predicts blue-shifted npi* and pipi* energies and stronger fluctuations compared to the other three force fields, which indicates that different force fields may predict different spectral lineshapes for proteins.
authors.affiliation: Department of Chemistry, University of California, Irvine, CA 92697 USA.
authors.forename: Zhenyu
authors.initials: Z
authors.lastname: Li
authors.forename: Haibo
authors.initials: H
authors.lastname: Yu
authors.forename: Wei
authors.initials: W
authors.lastname: Zhuang
authors.forename: Shaul
authors.initials: S
authors.lastname: Mukamel