OpenMMDL

OpenMMDL is a workflow that enables the setup, simulation, and analysis of OpenMM molecular dynamics simulations of protein-ligand complexes.

Availability

Cluster	Module/Version
BOSE	openmmdl/1.3.0
BGSC	None

Note: You can simply use module load openmmdl to activate the most recently installed version of this software.

Commands

Much of the documentation was compiled from the official GitHub page, so please follow the documentation links for more detailed explanation, usage and documentation.

Command	Description	Online Manual
setup	OpenMMDL Setup will allow you to prepare the files needed to perform a protein-ligand complex MD simulation with OpenMM.	Documentation
simulation	OpenMMDL Simulation starts the MD simulation with the inputs acquired from OpenMMDL Setup.	Documentation
analysis	OpenMMDL Analysis performs an analysis of the MD simulation obtained from OpenMMDL Simulation.	Documentation
visualization	Note: Most of the analysis outputs are JPEG images and do not need any further preparation to be viewed.	Documentation

Sample Slurm Script

submit.sh

#!/bin/bash
# -- SLURM SETTINGS -- #
# [..] other settings here [..]

# The following settings are for the overall request to Slurm
#SBATCH --ntasks-per-node=32     # How many CPU cores do you want to request
#SBATCH --nodes=1                # How many nodes do you want to request

# -- SCRIPT COMMANDS -- #

# Load the needed modules
module load openmmdl/1.3.0    # Load OpenMMDL
openmmdl simulation -f {path/to/folder_name} -t {path/to/topology} -s {path/to/script} -l {path/to/ligand}

Real Example

Has your research group used OpenMMDL in a project? Contact the HPC Team and we'd be glad to feature your work.

Citation

Talagayev, V., Chen, Y., Doering, N. P., Obendorf, L., Denzinger, K., Puls, K., Lam, K., Liu, S., Wolf, C. A., Noonan, T., Breznik, M., Knaus, P., & Wolber, G. (2025). OpenMMDL - Simplifying the Complex: Building, Simulating, and Analyzing Protein–Ligand Systems in OpenMM. Journal of Chemical Information and Modeling, 65(4), 1967–1978. https://doi.org/10.1021/acs.jcim.4c02158