生物分子的水合作用層如蛋白質與去氧核糖核酸，在其構形與生物功能的決定上伴演關鍵性的角色。將水分子包裝在蛋白質週圍之最小能量平衡穩定的構形可以使用分子力學加以確認。現有方法不是包裝太多水分子就是固定水合作用層的厚度。當包裝太多水分子時會耗費太多的計算時間，而固定水合作用層的厚度可以有效減少水分子的數目並且解決此問題。然而固定水合作用層的厚度會導致介於水合作用層水分子與團塊水分子之間的缺口。因此我們需要新的填水方法。本論文提出新填水方法所需的起始步驟。我們探討現有水分子模型與計算其凡得瓦爾半徑。現有水分子模型包含三址、四址與五址水分子模型。我們計算三址水分子模型單一球體與三重球體的凡得瓦爾半徑，還有四址水分子模型單一球體、三重球體與四重球體的凡得瓦爾半徑，以及五址水分子模型單一球體、三重球體與五重球體的凡得瓦爾半徑。然後將計算結果加以比較。

　　The hydration shell of a biological molecule, e.g., protein and DNA, plays a crucial role in determining their conformations and biological functions. The equilibrium conformation of a protein submerged in its hydration shell can be identified using molecular mechanics, which in turn requires packing water molecules to surround the protein. Existing methods either pack by far too many water molecules or fix the thickness of the hydration shell. While packing too many water molecules wastes too much computation time, fixing the shell thickness dramatically reduces the number of water molecules and resolves that problem. However, the fixed thickness results in gaps between shell water molecules and bulk water molecules. A new water packing method is needed. This thesis presents results of the initial step of a new water packing method. We review existing water models and determine the van der Waals radii. Existing water models consist of three-site, four-site, and five-site models. Correspondingly, we calculate single-sphere van der Waals radii and triple-sphere radii for three-site models, we do single-sphere radii, triple-sphere radii and quadruple-sphere radii for four-site water models, and we obtain single-sphere radii, triple-sphere radii and five-sphere radii for five-site water models. Calculation results are compared.

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