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.

Molecular Dynamics Simulation of the Interaction within the Carboxymethyl Cellulose-Modified Montmorillonite Lamellae at Aggressive CuCl2 Concentrations

“…A simulation box measuring 20.6 nm × 17.9 nm × 7.9 nm ( x × y × z ) was created using the Atomistic Topology Operation in the MATLAB (atom) package, with MMT clay lamella positioned on the one side, a CMC chain located at the center, and compensating sodium cations (from both MMT and CMC) randomly distributed within the interlayer space (Figure ). The box was then solvated with 83,772 SPC/E water molecules, resulting in a system comprising about 288,000 atoms in total with a polymer to clay mass ratio ( m CMC / m clay ) of 4.1%, which closely matched the laboratory-manufactured CMC-modified MMT ( m CMC / m clay = 5%) and the water content ( m water / m clay ) of 246%.…”

Molecular insights into the temperature and pressure dependence of mechanical behavior and dynamics of Na-montmorillonite clay

“…To construct a well-ordered structure file with proper atom typing, an open-source library of modular MATLAB routines called atomistic topology operations in MATLAB (atom) was employed. 56 This library facilitated several functions, including model building, manipulation, and structural analysis. Moreover, it enabled the use of the bond valence method and a neighbor-distance analysis to determine various chemical properties of inorganic molecules.…”

Structural and Dynamic Insights into SARS-CoV-2 Spike-Protein–Montmorillonite Interactions

“…The atomistic model of montmorillonite (MMT) surface was designed with Atomistic Topology Operations in MATLAB’s atom 40 package. A unit cell with a basic formula as Al 2 Si 4 O 10 (OH) 2 is replicated in X and Y directions.…”