EasyHybrid: An Interactive Graphical Environment for Quantum, Classical and Hybrid Simulations with pDynamo3

Abstract

We present EasyHybrid, a free and open-source graphical interface for hybrid quantum chemical/molecular mechanical (QC/MM) simulations built on the pDynamo3 library. The software provides an intuitive environment for preparing, inspecting, and editing molecular systems, while supporting a broad range of simulations, including reaction coordinate scans, molecular dynamics, normal-mode analysis, Nudged Elastic Band, and umbrella sampling. Key features include advanced 3D visualization of large biomolecular systems, interactive editing, flexible atom selection, system pruning for efficient QC/MM setup, orbital and electrostatic potential surfaces, automated log parsing, and trajectory analysis. EasyHybrid integrates these tools into a single platform, offering a familiar yet specialized environment for quantum chemistry and hybrid QC/MM simulations.

1

Overview of the EasyHybrid interface. The figure shows a hybrid QC/MM system, where the MM region is represented by lines and the QC region by ball-and-stick. The peptide backbone is highlighted using a thick stick representation (Cα trace), and the blue and red mesh depicts the highest occupied molecular orbital (HOMO).

2

QC region selection and setup in EasyHybrid: (a) atom selection in viewing mode with access to the Quantum Chemistry Setup window via the right-click menu; (b) configuration of QC parameters; (c) default representation of QC atoms as ball-and-stick and MM atoms as lines.

3

Potential energy surface (PES) scan along two reaction coordinates performed simultaneously. (a) Energy matrix plot, where the horizontal (x) and vertical (y) axes correspond to reaction coordinates r1 and r2, respectively. Labels for reactants (R), transition state (TS), and products (P) were added later during figure composition. The user can interactively select frames from the energy surface to generate (b) a one-dimensional energy profile, facilitating analysis as a reaction trajectory. Alternative reaction paths can be analyzed by selecting a different sequence of frames, such as the apparent pathway through the lower right corner of the PES (which, in this case, is an artifact). Representative structures are shown for (c) reactants, (d) transition state, and (e) products. Markers 1, 2, and 3, centered on semitransparent spheres, indicate the selected atoms (picking mode) that define the reaction coordinates, while dashed lines show the interatomic distances dynamically tracked along the trajectory. Energies were calculated using the hybrid AMBER ff99S/PM6 model. All plots were generated with EasyPlot.