The molecule being displayed by VMD is the subject of a recent TB paper, a channel responsible for the transmission of water across cell membranes.
You can see a simpler representation of the channel (or go back to the original view.)
Show the water that is inside and around the channel (or hide it again.) Notice that the water molecules move through the channel in single file.
In addition to water, this channel also allows small sugar molecules such as glycerol (hide it) to pass. However, it is very good at preventing other small molecules from getting through. The narrowest part of the channel (hide it) acts as a filter to exclude the unwanted molecules. You can use the mouse to look straight down the channel and get an idea of how narrow the filter region is.