Paper Citing NAMD - Abstract
Lee, O.S.; Saven, J.G.
Simulation studies of a helical m-phenylene ethynylene foldamer
JOURNAL OF PHYSICAL CHEMISTRY B, 108:11988-11994, AUG 12 2004
The folded state of an oligo(m-phenylene ethynylene) foldamer solvated in water is examined using a 30 ns NpT molecular dynamics simulation. The 18-monomer oligomer with methyl ester exterior side groups maintains a helical structure, where turns of the helix are in close contact throughout the simulation. The structure exhibits large fluctuations in both the radius of the interior cylindrical pore and the effective dihedral angle between monomers. The radius fluctuations are correlated with the number of water molecules within the helical pore. The folded state is found to be surprisingly flexible while maintaining a helical structure.
