GRADE: A code to determine clathrate hydrate structures

Abstract

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 512, 62512 and 64512 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 F4 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. Program summaryProgram Title: GRADEProgram Files doi:http://dx.doi.org/10.17632/h8d7zgmchf.1Licensing provisions: GNU GPLv3Programming language: C++Nature of problem: Analyze gas clathrate formation from atomic positions of water molecules in computer simulationsSolution method: Algorithms to find 512, 62512 and 64512 cages and calculate F4 order parameter