MonicaMD: Molecules and Internal Cluster Analysis of Molecular Dynamics Simulations

Molecular dynamics (MD) simulations are a widely applied tool to investigate systems of varying complexity, from isolated molecules to biomolecules consisting of many thousands of atoms. Extracting mechanistic insights from the high-dimensional data sets frequently presents a challenge. Here, we introduce the publicly available MOlecules aNd Internal Cluster Analysis of Molecular Dynamics simulations (MonicaMD) program package, a versatile and efficient tool that targets the analysis of molecules and molecular clusters in atomistic classical and semiclassical trajectories. MonicaMD provides modular access to structural information, with a focus on internal and collective variables. A further key functionality is the extraction of electrostatic information. MonicaMD offers a user-friendly workflow including dimensionality reduction, automatic feature-space generation, and a templating functionality for generated grids in order to be readily used in conjunction with quantum chemical software and machine learning frameworks. The functionality of MonicaMD offers the user a convenient and efficient bridge between classical MD and higher-accuracy quantum mechanics simulations. This synergy enabled by MonicaMD is demonstrated by the investigation of conformational analysis in a protein–ligand complex, structural and electrostatic effects of DNA intercalation, and the excited-state isomerization of a photoswitch. Additional examples include reactive coordinates of a transition-metal-catalyzed C–N coupling reaction and of the light-initiated generation of free diazoalkane, as well as an analysis of chlorophyll binding sites in a photosynthetic complex.