Paper Citing NAMD - Abstract
Su, Guoxiong; Czader, Arkadiusz; Homouz, Dirar; Bernardes, Gabriela; Mateen, Sana; Cheung, Margaret S.
Multiscale Simulation on a Light-Harvesting Molecular Triad
JOURNAL OF PHYSICAL CHEMISTRY B, 116:8460-8473, JUL 26 2012
We have investigated the effect of solvation and confinement on an artificial photosynthetic material, carotenoid-porphyrin-C-60 molecular triad, by a multiscale approach and an enhanced Sampling technique. We have developed a combined approach of quantum chemistry, statistical physics, and all-atomistic molecular dynamics Simulation to determine the partial atomic charges of the ground-state triad. To fully explore the free energy landscape of triad, the replica exchange method was applied to enhance the sampling efficiency of the simulations. The confinement effects on the triad were modeled by imposing three sizes of spherocylindrical nanocapsules. The triad is structurally flexible under ambient conditions, and its conformation distribution is manipulated by the choice of water models and confinement Two types of water models (SPC/E and TIP3P) are used for solvation. When solvated by SPC/E water, whose HOH angle follows an ideal tetrahedron, the structural characteristics of triad is compact in the bulk systems. However, under a. certain nanosized. confinement that drastically disrupts hydrogen bond networks in solvent, the triad favors an extended configuration By contrast, the triad solvated by TIP3P water shows a set of U-shaped conformations in the confinement We have shown that a slight structural difference in the two water models with the same dipole moment can have great distinction : in water density, water orientation, and the number of hydrogen bonds in the proximity of a large flexible compound such as the triad. Subsequently, it has direct impact on the position Of the triad in a confinement as well as the distribution of conformation's at the interface of liquid and Solid. in a finite size system.
