drMD

Automated workflow for running molecular dynamics simulations with Amber and Openmm

Installation

Create and activate conda environment

conda create -n drMD python=3.10

conda activate drMD

Install AmberTools (needs to be before OpenMM)

conda install -c conda-forge ambertools=23

Install OpenMM

conda install -c omnia openmm

Install other python libraries

pip install argpass pyyaml pandas propka

Clone this repository

git clone https://github.com/ESPhoenix/drMD.git

Usage

Run example pdbs

python path/to/drMD/batch_drMD.py --bc path/to/drMD/batch_config.yaml

To run your own pdb files, modify batch_config.yaml file