lindemann is a python package to calculate the Lindemann index of a lammps trajectory

A batteries-included toolkit of analysis modules and helper functions for molecular dynamics (MD) simulations.

molecule builder for LAMMPS in Julia

This repository contains Python scripts to analyze MD & PELE simulations, to preprocess & process the system (pdb files), and many more.

FELBuilder is an automated Python pipeline that automates the complex workflow of Principal Component Analysis (PCA) and Free Energy Landscape (FEL) analysis from Molecular Dynamics (MD) trajectories.

Calculates change of H bond frequency (stability), average angle and average distance from cpptraj hbond output files and creates a sortable, color coded excel table. The Alignkeys submodule was created by excelforum user shg.

Molecular Dynamics From Scratch: a from-zero, educational MD engine built on JAX and OpenMM, with CUDA-12 wheels, pytest validation, and a learning path that walks through forcefields, integrators, and analysis primitives.