Earlier studies using X-ray diffraction, light scattering, photon correlation spectroscopy, and atomic force microscopy, strongly suggest that SNARE-induced membrane fusion in cells proceeds as a result of calcium bridging opposing bilayers. The bridging of phospholipid heads groups in the opposing bilayers by calcium leads to the release of water from hydrated Ca2+ ions as well as the loosely coordinated water at PO-lipid head groups. Local dehydration of phospholipid head groups and the calcium, bridging opposing bilayers, then leads to destabilization of the lipid bilayers and membrane fusion. This hypothesis was tested in the current study by atomistic molecular dynamic simulations in the isobaric—isothermal ensemble using hydrated dimethylphosphate anions (DMP−) and calcium cations. Results from the study demonstrate, formation of DMP—Ca2+ complexes and the consequent removal of water, supporting the hypothesis. Our study further demonstrates that as a result of Ca2+–DMP self-assembly, the distance between anionic oxygens between the two DMP molecules is reduced to 2.92 Å, which is in close agreement with the 2.8 Å SNARE-induced apposition established between opposing bilayers, reported earlier from X-ray diffraction measurements.