Paper Citing NAMD - Abstract
Chiu, Chi-cheng; DeVane, Russell; Klein, Michael L.; Shinoda, Wataru; Moore, Preston B.; Nielsen, Steven O.
Coarse-Grained Potential Models for Phenyl-Based Molecules: II. Application to Fullerenes
JOURNAL OF PHYSICAL CHEMISTRY B, 114:6394-6400, MAY 20 2010
The interaction of fullerenes with biological systems and the environment is a topic of current interest. Coarse-grained molecular dynamics (CGMD) simulations are well-suited to investigate some of the factors involved because they provide access to time and length scales that are not accessible using fully atomistic simulation methods. In the case of buckyballs (C(60)) and single-walled carbon nanotubes (SWNTs), it is necessary to parametrize a CG force field that accurately captures the balance between fullerene-fullerene and fullerene-solvent interactions. Herein, we derive CG force field parameters for C(60) and SWNTs by using the optimized benzene parameters from part I [DeVane, R.; Chiu, C.-c.; Nielsen, S. O.; Shinoda, W.; Moore, P. B.; Klein, M. L. J. Phys. Chem. B 2010, doi: 10.1021/jp9117369]. Solubility, transfer free energy, and dimerization free-energy data for C(60) and SWNTs obtained using the proposed models show excellent agreement with experimental and fully atomistic MD data. In particular, cluster analysis of C(60) aggregation in a hydrocarbon melt corroborates the force field parameters. The aggregation behavior of the present CG force field differs considerably from that of models currently in widespread use. The combined results provide a strong basis for applying this model for further large-scale MD studies involving C(60) and SWNTs.
