ehmdee: Molecular Dynamics Simulation with OpenMM

This program is a Python script that runs a Molecular Dynamics (MD) simulation using the OpenMM library. It is designed to be run from the command line and accepts several arguments that allow you to customize the simulation. This program was designed with outputs from Alphafold multi-chain models in mind, but it should work with any PDB file.

Getting Started

To run the simulation, navigate to the directory containing the script and run:

python ehmdee.py --input input.pdb --output output.pdb --use_gpu --solvent --minimize --timesteps 10000 --report_interval 100

Command-line Arguments

• --input: Path to the input file in PDB format.
• --output_path: Path to save the output file.
• --use_gpu: Use GPU for the simulation.
• --solvent: Add solvent to the simulation.
• --minimize: Minimize the energy of the system before running the simulation.
• --timesteps: Number of time steps to run in the simulation.
• --report_interval: Interval at which to report simulation data.

Simulation Demonstration