Google Colab notebooks for running molecular dynamics simulations with GROMACS

Set up relative free energy calculations using a common scaffold

Automatic CHARMM-GUI browser interaction with Python

This code adds custom-made amino acids to the GROMACS forcefield directory.

Tutorial for converting NAMD psf/pdb files to CHARMM PSF/CRD (credit attributed where appropriate to the AMAZING humans who developed these scripts)

A multi-purpose tool for automated setup of MD systems (e.g. for transformato) and local, menu-based rerunning of CHARMM-GUI input scripts for CHARMM

Analysis scripts for the CHARMM GUI Drude Prepper Paper

A Molecular Dynamics simulation project of pyrazinamidase studying its influence in antibiotic resistance of pyrazinamide. The TIP3P water model as implemented in CHARMM (MacKerell) specifies a 3-site rigid water molecule with charges and Lennard-Jones parameters assigned to each of the 3 atoms. In GROMACS the fix shake command can be used to ho…

I present tools that accelerate molecular dynamics (MD) simulations using NAMD software and support the analysis of the obtained trajectories.

ASOs in LNPs with receptor-guided permeation

Scripts to help with setting up molecular dynamics simulations.

A reproducible, end-to-end computational pipeline that uses a machine-learning docking surrogate and receptor-aware fragment growing to design a new Nrf2-inhibitor candidate, followed by force-field parametrization, explicit-solvent energy minimization, and AI-assisted retrosynthetic assessment.