Besides phosphatidylcholines and cholesterol, sphingomyelin molecules are the most important lipid species in the biological membranes, and their role has recently been emphasized in various membrane phenomena, such as domain formation. Here, a multinanosecond molecular dynamics (MD) simulation study was performed at physiological temperature for a hydrated bilayer system, consisting of 128 palmitoylsphingomyelin (16: 0-SM) molecules. Analysis of the structural parameters of the system indicates that 16:0-SM bilayer is in a mixed state of liquid-crystalline and condensed phases, which results in considerable ordering in the hydrocarbon chain region. The simulation also revealed major differences in the hydrogen-bonding properties between the sphingomyelin and phosphatidylcholine molecules. In the future, MD simulation studies are also likely to shed light on the detailed structural properties of the lateral membrane domains of mammalian cells, termed rafts, which form because of association of sphingolipids and cholesterol.