md-simulation

Software for automated molecular dynamics exploration

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.

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.

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.

Build solvated glycosylated protein systems for GROMACS using open-source AMBER tooling. Worked example: IgG1 Fc (PDB 3AVE).

LAMMPS MCP server for molecular dynamics: an AI agent runs LAMMPS/ReaxFF jobs, inspects and renders trajectories. macOS app + CLI, GPU cloud tier.

MDSimulator: Python-tkinter GUI for automating GROMACS molecular dynamics simulations — topology generation, solvation, ion addition, energy minimisation, equilibration, and production MD — registered IP (IPO Pakistan, 2023)

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.

GROMOS molecular-dynamics simulations of biomolecular system: force-field parametrization, β-peptide & protein dynamics, liquid properties, alchemical free energies (thermodynamic integration), and NMR/NOE structure refinement, each benchmarked against experiment.

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.