Paper Citing NAMD - Abstract
Li, Zhenyu; Yu, Haibo; Zhuang, Wei; Mukamel, Shaul
Geometry and excitation energy fluctuations of NMA in aqueous solution with CHARMM, AMBER, OPLS, and GROMOS force fields: Implications for protein ultraviolet spectra simulation
CHEMICAL PHYSICS LETTERS, 452:78-83, FEB 4 2008
Molecular dynamics (MD) simulations are performed for N-methylacetamide (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 n pi* and pi pi* transition energies as quadratic functions of the NMA geometric variables is used to simulate the excitation energy fluctuations. GROMOS96 predicts blue shifted n pi* and pi pi* energies and stronger fluctuations compared to the other three force fields, which indicates that different force fields may predict different spectral lineshapes for proteins. (c) 2007 Elsevier B.V. All rights reserved.
