GROMACS-on-Colab

This repository provides four notebooks for running molecular dynamics simulations on Google Colab.

• Build_to_Google_Drive.ipynb
  Installs GROMACS to your Google Drive, where it can be loaded by the other notebooks.
  

• GROMACS_for_CHARMM-GUI.ipynb
  Equilibrates a system prepared with CHARMM-GUI. This notebook unpacks a CHARMM-GUI.tgz archive from "Solution Builder." Optionally, it can merge in an archive from "Ligand Reader," allowing for piecewise preparation of protein-ligand systems.
  

• GROMACS_for_production.ipynb
  Starts or resumes a production simulation.
  

• Trajectory_analysis_tools.ipynb
  Calculates data that can be derived from a production simulation trajectory, such as centroid structures, RMSDs, and interaction energies.
  

All inputs and outputs are stored on your Google Drive.