atom: A Matlab Package for Manipulation of Molecular Systems

• DOI: 10.1007/s42860-019-00043-y
• Publication Date: 2020-01-17T10:02:57Z
• Authors: Michael Holmboe
• Keywords: File format; Interface (matter)

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