GRADE: A code to determine clathrate hydrate structures

GRADE is an open-source software package that identifies clathrate hydrate structures given the atomic coordinates of oxygen atoms of water. These structures are commonly found in natural gases and they are relevant to understand antifreezing proteins as well as the hydrophobic effect. In this manuscript, we describe basic algorithms used by GRADE to determine 5^12, 6^2 5^12 and 6^4 5^12 water cages. These algorithms are based on the connectivity of five and six-folded rings made of first-neighbor water molecules. Schemes to speed up the calculation of these cages are discussed and implemented in the code. GRADE also computes the four-body order parameter F_4 commonly used to identify different phases of water. An example of how GRADE can be used to compute the spontaneous nucleation of methane clathrates is also provided.

GRADE是一款开源软件包，旨在根据水分子氧原子的原子坐标识别笼状水合物结构。此类结构广泛存在于天然气中，对于理解抗冻蛋白以及疏水效应具有重要意义。在本篇论文中，我们详细阐述了GRADE所使用的确定5^12、6^2 5^12及6^4 5^12水笼的基本算法。这些算法基于由相邻水分子构成的五边形和六边形环的连接性。同时，我们也讨论并实现了加速这些水笼计算方案。GRADE还能计算四体序参量F_4，该参量常用于识别水的不同相态。此外，我们还提供了一个如何使用GRADE计算甲烷笼状水合物自发的成核过程的实例。