atom: A MATLAB PACKAGE FOR MANIPULATION OF MOLECULAR SYSTEMS

Abstract

This work presents Atomistic Topology Operations in MATLAB (atom), an open source library of modular MATLAB routines which comprise a general and flexible framework for manipulation of atomistic systems. The purpose of the atom library is simply to facilitate common operations performed for construction, manipulation, or structural analysis. Due to the data structure used, atoms and molecules can be operated upon based on different chemical names or attributes, such as atom- or molecule-ID, name, residue name, charge, positions, etc. Furthermore, the Bond Valence Method and a neighbor-distance analysis can be performed to assign many chemical properties of inorganic molecules. Apart from reading and writing common coordinate files (.pdb,.xyz,.gro,.cif) and trajectories (.dcd,.trr,.xtc; binary formats are parsed via third-party packages), the atom library can also be used to generate topology files with bonding and angle information taking the periodic boundary conditions into account, and supports basic Gromacs, NAMD, LAMMPS, and RASPA2 topology file formats. Focusing on clay-mineral systems, the library supports CLAYFF (Cygan, 2004) but can also generate topology files for the INTERFACE forcefield (Heinz, 2005, 2013) for Gromacs and NAMD.