This tutorial covers two recent (added in 2020) developments for OpenPathSampling. These are the new (experimental) storage subsystem, called SimStore, and the command line interface to OPS.
Note that these topics are independent -- the CLI can also be used with the old storage subsystem (NetCDFPlus) and SimStore can be used without the CLI. However, performance improvements in SimStore make it much more convenient for the kind of interactivity enabled by the CLI.
In OPS 2.0, NetCDFPlus will be removed and SimStore will be used for all storage.
This tutorial was presented as a series of three YouTube videos. You can watch them in the playlist for this tutorial [COMING SOON], or you can watch each part:
- Part 1: Setting up with SimStore
- Part 2: Running simulations with the CLI
- COMING SOON: Part 3: Analyzing the results
This tutorial requires OpenPathSampling 1.5 or later and the OpenPathSampling CLI 0.2 or later. In addition, it requires OpenMM and OpenMMTools. Finally, SQLAlchemy and dill must be installed for SimStore to work.
Install the requirements with:
conda install -c conda-forge openpathsampling openpathsampling-cli
conda install -c conda-forge openmm openmmtools
conda install -c conda-forge sqlalchemy dillIn addition, you will need about 500 MB of disk space available.
The tutorial consists of Jupyter notebooks (for setup and analysis) as well as a Markdown file describing what needs to be done to run with the CLI. We recommend either using a terminal within JupyterLab to run the CLI commands, or keeping a separate terminal open on your system.
The tutorial can also be run on Binder, via its JupyterLab interface.
The setup process is described in the notebook 1_simstore_setup.ipynb. The
process of using the CLI is described in 2_running_cli.md. The analysis is performed
in 3_analysis.ipynb.