Welcome to seekrflow’s documentation!

Seekrflow is a workflow management system for molecular simulations using seekr. It automates the complex process of setting up, running, and analyzing molecular kinetics calculations.

Key Features:

  • Automated workflow from system parameterization to running simulations

  • Seekr stages may be run locally or on remote high-performance computing resources

  • Automatically parameterize a molecular system with a standard force field (if you dare!)

  • API may be used for batch seekr job creation and submission

Getting Started

Install seekrflow and get up and running quickly with a basic example.

To the Getting Started Guide

Tutorials

Step-by-step tutorials covering common workflows and advanced features.

To the Tutorials

User Guide

Comprehensive guide covering all aspects of using seekrflow.

To the User Guide

API Reference

Complete technical reference for all modules, classes, and functions.

To the API Reference

Developer Guide

Learn how to contribute to seekrflow and extend its functionality.

To the Developer Guide

Quick Start Example

Once seekrflow, SEEKR2, and SeekrTools are installed, a full example workflow requires only a PDB files containing a protein and a bound ligand, a configuration JSON file, and the resname of the ligand. The example can be run with the following commands:

cd ~/seekrflow/examples/trypsin_benzamidine/
python ~/seekrflow/seekrflow/parameterize.py protein_ligand.pdb --input_json seekrflow.json --ligand_resname BEN
python ~/seekrflow/seekrflow/flow.py seekrflow.json prepare
python ~/seekrflow/seekrflow/flow.py seekrflow.json run
python ~/seekr2/seekr2/analyze.py work/root/model.xml

For detailed installation instructions, see the Getting Started guide.