molUP

molUP facilitates preparation and analysis of Gaussian quantum chemistry calculations and ONIOM workflows within Visual Molecular Dynamics (VMD) to support studies of reaction mechanisms.

Key Features:

• VMD integration: Integrates into Visual Molecular Dynamics (VMD) and supports opening and saving Gaussian file formats.
• QM calculation setup: Facilitates preparation of quantum mechanics (QM) calculations including ONIOM hybrid methods such as QM/MM, QM/QM, and QM/QM/MM.
• Structure import: Imports starting structures from multiple chemical file formats for use in QM and ONIOM setups.
• Geometry manipulation: Provides tools to modify bond lengths, rotate bond angles, adjust dihedral angles, and add or remove atoms or molecules.
• ONIOM layer definition and fixed-atom selection: Defines ONIOM layers and supports selection of fixed atoms during geometry optimizations.
• Charge recalculation and advanced calculations: Supports atomic charge recalculation and setup of Scan (SCAN) and Intrinsic Reaction Coordinate (IRC) calculations.
• Gaussian output analysis: Extracts geometries and energies from Gaussian output files for downstream analysis.

Scientific Applications:

• Reaction mechanism studies: Supports setup and analysis of calculations (including IRC and Scan) used to characterize reaction pathways and mechanisms.
• Multiscale QM modeling: Enables ONIOM-based QM/MM, QM/QM, and QM/QM/MM modeling for multiscale computational chemistry problems.
• Gaussian input/output workflows: Assists in preparing Gaussian input files and extracting results from Gaussian outputs for computational (bio)chemistry investigations.

Methodology:

Preparation of Gaussian input files; definition of ONIOM layers for QM/MM, QM/QM and QM/QM/MM; import of starting structures; interactive geometry edits (bond, angle, dihedral adjustments and atom/molecule addition or removal); selection of fixed atoms for geometry optimizations; atomic charge recalculation; setup of Scan (SCAN) and IRC calculations; extraction of geometries and energies from Gaussian output files.