This repository contains the scripts (code) and data demonstrating the applications of IMDv3 streaming for the manuscript titled "Streaming Molecular Dynamics Simulation Data for On-the-fly Processing and Analysis" (update with actual title and doi). The manuscript is currently under review and the data and scripts are provided here for transparency and reproducibility.
The 3 examples contained in this repository, each use different simulation engines. The applications are described in detail in the Applications python notebook. The actual simulation+streaming can be run as described in the notebook using the scripts in the respective sample simulation folder - run-slurm.sh. The corresponding data from these streaming applications is provided in the respective output folders - paper/sample_simulation/MD-engine/output/. The *.csv files in these folders contian data used for the IMDv3-applications plot in the manuscript.
Lastly, we have provided a live analysis and visualization implmentataion in a Jupyter notebook interface for the NAMD simulation example shown above. The notebook can be run by following the instructions contained within it, along with the necessary scripts to run the simulation. Other applications can also be easily extended to use the live visualization setup if needed.