Open Source Repo for Molecular Dynamics Analysis Scripts
This repository contains a collection of scripts for analyzing and visualizing molecular dynamics simulations. These scripts are not intended to work "out of the box" but rather as a starting point for creating your own analysis scripts.
- [RMSF analysis]
Measure per-residue RMSF for a simulation. This can be used to determine specific regions of a protein that are undergoing conformational changes. Particularly useful when comparing Wild-Type vs Mutant structures.
- [RMSD analysis]
Measure the RMSD of a selection of residues over time. This can be used to determine if any significant conformational changes have occurred during a simulation.
- [Hydrogen bond analysis]
Measure the distance and angle between hydrogen bonds over time. This can be used to determine whether specific residues are forming hydrogen bonds with other residues.
- [Water bridge detection]
Detect water bridges in a simulation. This can be useful for finding interactions that would otherwise be missed by classical hydrogen bond analysis.