Paper Citing NAMD - Abstract
DeVane, Russell; Klein, Michael L.; Chiu, Chi-cheng; Nielsen, Steven O.; Shinoda, Wataru; Moore, Preston B.
Coarse-Grained Potential Models for Phenyl-Based Molecules: I. Parametrization Using Experimental Data
JOURNAL OF PHYSICAL CHEMISTRY B, 114:6386-6393, MAY 20 2010
A coarse-grained intermolecular potential has been parametrized for phenyl-based molecules. The parametrization was accomplished by fitting to experimental thermodynamic data. Specifically, the intermolecular potentials, which were based on Lennard-Jones functional forms, were parametrized and validated using experimental surface tension, density, and partitioning data. This approach has been used herein to develop parameters for coarse-grained interaction sites that are applicable to a variety of phenyl-based molecules, including analogues of the amino acid side chains of phenylalanine and tyrosine. Comparison of the resulting coarse-grain model to atomistic simulations shows a high level of structural and thermodynamic agreement between the two models, despite the fact that no atomistic simulation data was used in the parametrization of the coarse-grain intermolecular potentials.
