Simulation of molecular dynamics of water movement in ion channels

The motion of water molecules in a gramicidin-like channel was studied by the molecular dynamics method. Water molecules are presented in the ST2 model. The structure of the channel was presented in the form of channel's helix frame possessing mobile dipole groups. The interaction of all mobile particles with the membrane channel's walls was taken into account. The calculation consisted of 50,000 integration steps of delta t = 5 x 10(-16) s which corresponded to a total elapsed time of 25 ps. It was shown that water molecules in the channel did not possess rigid spatial structure but exhibited a structure oriented along the channel axis. The motion of water molecules in the channel occurred smoothly, i.e. all water molecules did not have any deep, stable potential wells in the channel. The distribution of water molecules along the radial coordinate of the channel was estimated. Water density was shown to be maximal near the channel axis.