Paper Citing NAMD - Abstract
Bucher, Denis; Kuyucak, Serdar
Importance of water polarization for ion permeation in narrow pores
CHEMICAL PHYSICS LETTERS, 477:207-210, JUL 28 2009
Molecular dynamics (MD) simulations are mostly performed using non-polarizable force fields. This approximation works in homogeneous systems but there are situations - such as pores, cavities and interfaces - where an explicit description of polarization may be necessary. Here, we perform density functional calculations and Car-Parrinello MD simulations to investigate the effect of polarization on solvated ions in narrow pores. Polarization of water molecules in the first hydration shell of a K(+) ion is found to be significantly larger in a narrow pore compared to that in bulk water. Implications of these observations on the energetics of ion permeation in narrow pores are discussed using simple models. (C) 2009 Elsevier B. V. All rights reserved.
