Paper Citing NAMD - Abstract
Zhu, F.Q.; Tajkhorshid, E.; Schulten, K.
Pressure-induced water transport in membrane channels studied by molecular dynamics
BIOPHYSICAL JOURNAL, 83:154-160, JUL 2002
A method is proposed to measure the water permeability of membrane channels by means of molecular dynamics simulations. By applying a constant force to the bulk water molecules and a counter force on the complementary system, a hydrostatic pressure difference across the membrane can be established, producing a net directional water flow. The hydraulic or osmotic permeability can then be determined by the ratio of the water flux and the pressure difference. The method is applied and tested on an aquaglyceroporin channel through a series of simulations totaling 5 ns in duration.
