# StreaMD Documentation

StreaMD is a toolkit for high-throughput molecular dynamics simulations that automates preparation, equilibration, production, and analysis. It supports protein-only, protein-ligand, and protein-cofactor systems, can resume interrupted runs, and includes built-in analysis plus MM/PB(GB)SA and ProLIF tooling.

```{toctree}
:maxdepth: 2
:caption: Contents

overview
installation
input_preparation
running_md
advanced_features
outputs
mm_pbsa
plif
trajectory_convergence
configuration
logging
changelog
license
citation
```