Paper Citing NAMD - Abstract
Petridis, Loukas; Smith, Jeremy C.
A Molecular Mechanics Force Field for Lignin
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30:457-467, FEB 2009
A CHARMM molecular mechanics force field for lignin is derived. parameterization is based on reproducing quantum mechanical data of model compounds. Partial atomic charges are derived using the RESP electrostatic potential fitting method supplemented by the examination of methoxybenzene:water interactions. Dihedral parameters are optimized by fitting to critical rotational potentials and bonded parameters are obtained by optimizing vibrational frequencies and normal modes. Finally, the force field is validated by performing it molecular dynamics simulation of it crystal of a lignin fragment molecule and comparing simulation-derived structural features with experimental results. Together with the existing force field for polysaccharides, this lignin force held Will enable full Simulations of lignocellulose. (C) 2008 Wiley Periodicals, Inc.
