MiMiCPy

MiMiCPy automates preparation and validation of MiMiC-compatible input files for QM/MM simulations that integrate CPMD and GROMACS to support multiscale modeling of biological systems.

Key Features:

• PrepQM subcommand: Generates MiMiC input files from the command line to define QM regions for QM/MM simulations.
• PyMOL and VMD plugins: Provide visual selection of QM regions and produce corresponding MiMiC input files.
• Automation of QM-region selection: Reduces manual preparation for large QM regions to decrease human error in input generation.
• Debugging and correction subcommands: Provide functions to detect and correct issues in MiMiC input files.
• Modular architecture: Enables integration and extension to additional program formats required by MiMiC.
• Implementation: Written in Python 3 with an object-oriented programming approach.

Scientific Applications:

• MiMiC-based QM/MM simulations: Preparation and validation of input files for combined quantum and molecular mechanics studies using CPMD and GROMACS.
• Multiscale modeling of biological systems: Enabling different regions of a system to be treated at varying levels of theoretical rigor.
• Large QM-region studies: Facilitating setup of simulations that require extensive QM regions to capture electronic effects.

Methodology:

Implemented in Python 3 with object-oriented design; provides the PrepQM subcommand to generate MiMiC input files from the command line or via PyMOL/VMD plugins for visual QM-region selection; includes subcommands for debugging and correcting MiMiC input files and a modular design for extending program formats.