Paper Citing NAMD - Abstract
Zhu, F.Q.; Tajkhorshid, E.; Schulten, K.
Theory and simulation of water permeation in aquaporin-1
BIOPHYSICAL JOURNAL, 86:50-57, JAN 2004
We discuss the difference between osmotic permeability p(t) and diffusion permeability p(d) of single-file water channels and demonstrate that the p(t)/p(d) ratio corresponds to the number of effective steps a water molecule needs to take to permeate a channel. While p(d) can be directly obtained from equilibrium molecular dynamics simulations, p(t) can be best determined from simulations in which a chemical potential difference of water has been established on the two sides of the channel. In light of this, we suggest a method to induce in molecular dynamics simulations a hydrostatic pressure difference across the membrane, from which p(t) can be measured. Simulations using this method are performed on aquaporin-1 channels in a lipid bilayer, resulting in a calculated p(t) of 7.1 x 10(-14) cm(3)/s, which is in close agreement with observation. Using a previously determined pd value, we conclude that p(t)/p(d) for aquaporin-1 measures similar to12. This number is explained in terms of channel architecture and conduction mechanism.
DOI:10.1016/S0006-3495(04)74082-5
