# Simulation workflows meeting

## Docking + free energy

Use stage to generate topologies
Combine to hybrid topology
Putting ligand into place - binding site alignment of two protein structures
AWH free energy calculation (single walker)
hyper-queue (how to match cluster resources to GROMACS expectations; issues on openMP threads, MPI ranks, IT4I)

## Which workflow tool to use?

- make
- snakemake
- nextflow
- biobb
- cwl (common workflow language)

## Preparing .mdp files with .mdp-editor

## Documenting workflow issues, identifying the largest road-blocks

Kenneth and Nandan did some great work already here:

https://hackmd.io/sJYhttfAQ7SCI-u96XcqzQ