Paper Citing NAMD - Abstract
Liu, Jian; Fan, Jianfen; Tang, Min; Cen, Min; Yan, Jianfeng; Liu, Zhao; Zhou, Weigun
Water Diffusion Behaviors and Transportation Properties in Transmembrane Cyclic Hexa-, Octa- and Decapeptide Nanotubes
JOURNAL OF PHYSICAL CHEMISTRY B, 114:12183-12192, SEP 30 2010
Molecular dynamics simulations have been performed on three transmembrane cyclic peptide nanotubes, i.e., 8 x (W (L) under barL)(n=345)/POPE (with uniform lengths but various radii) to investigate the radial dependences of the water-chain structures, diffusions, and transportation properties. The diffusions of individual water molecules and collective coordinates of all the channel-water in the three systems are certified as unbiased Brownian motions. From the very good linear relationships between MSDs and time intervals, the diffusion coefficients and transportation permeabilities have been deduced efficiently. Under the hydrostatic pressure differences across the membrane, a net unidirectional water flow rose up, and the osmotic permeabilities were determined. The ratios of the osmotic and diffusion permeabilities (p(f)/p(d)) were examined for all the three channels.
