qmmm

Sire Molecular Simulations Framework

PaCS-Q is a Python toolkit designed to assist with Parallel Cascade Selection simulations (PaCS) for studying protein structural transitions in MD and QM/MM MD level.

Collection of tools for running MD, QM, and QM/MM calculations

NAMD-xtb-QMMM-interface

↪️ QM/MM interfacing in Python ↩️

QM/DMD engine. Protein Hybrid Discrete Dynamics/DFT

Python interface for subtractive QM/MM calculations with AMOEBA polarizable force field using Gaussian16 and Tinker.

RCBS.py (Reactivity of Chemical and Biochemical Systems) is a Python package that contains several scripts, functions and classes that simplify the analysis of chemical and biochemical simulations.

Code for training and running reactive molecular dynamics and QM/MM simulations

Mirror of pDynamo computational chemistry library

An open-source QM/MM interface coupling DFTB+ with GROMACS for energy-conserving ground-state molecular dynamics

Scripts used in the Chemistry bachelor's thesis project about the positional regioselectivity of human ALOX15

Gaussian + LAMMPS + ASE implementation to perform optimization, NEB and metadynamics calculations

Universal Peptide Drug Discovery — AI-driven cyclic peptide design pipeline with ncAA integration

Combination of Gaussian ONIOM and ASE to perform QMMM calculations: geometry optimization and finding transition states using NEB

Supporting information for the Master's thesis: "QM/MM Studies of Ni- and Fe-rubredoxin"

Predicted and Experimental NMR Chemical Shifts at Variable Temperatures: The Effect of Protein Conformational Dynamics