Paper Citing NAMD - Abstract
De Fabritiis, G.; Coveney, P. V.; Villa-Freixa, J.
Energetics of K(+) permeability through Gramicidin A by forward-reverse steered molecular dynamics
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 73:185-194, OCT 2008
The estimation of ion channel permeability poses a considerable challenge for computer simulations because of the significant free energy barriers involved, but also offers valuable molecular information on the ion permeation process not directly available from experiments. In this article we determine the equilibrium free energy barrier for potassium ion permeability in Gramicidin A in an efficient way by atomistic forward-reverse non-equilibrium steered molecular dynamics simulations, opening the way for its use in more complex biochemical systems. Our results indicate that the tent-shaped energetics of translocation of K(+) ions in Gramicidin A is dictated by the different polarization responses to the ion of the external bulk water and the less polar environment of the membrane.
