Getting Started

Installation

The “installation” of reForge consists of including the reForge project directory in your Python path and ensuring that you have all the necessary dependencies. All the packages that reForge depends on, except for GROMACS, can be installed with conda and/or pip.

Warning

For users of SOL and PHX clusters: For more detailed instructions, scroll down the page.

  1. Clone the repository:

    This will create the directory “reforge” in your current directory.

git clone https://github.com/DanYev/reforge.git

  1. Install the virtual environment:

cd reforge
conda env create -n reforge --file environment.yml
source activate reforge

  1. Include reForge in your Python path OR install it via pip:

export PYTHONPATH=$PYTHONPATH:path/to/reforge/repository
# or
pip install -e . # from the reForge repository directory

Testing the Setup

From the reForge repository directory, you can run the tests with the following command:

cd path/to/reforge/repository
bash run_tests.sh --all

Running the Examples

At the moment, the coarse-grained examples can only be run with GROMACS. OpenMM support is in active development. Thus, to run the tutorials, you need to have GROMACS installed on your system. Some basic examples can be found here: examples, and will be updated as the project progresses.

For SOL and PHX Users

Warning

Please read this carefully before proceeding! Start with a clean shell and DO NOT activate any environments or interactive sessions unless stated in the instructions. Run the commands EXACTLY as they are in the instructions. Starting an interactive session or running commands with “bash” instead of “source” (.) initiates a new, separate shell process with different environment variables and may break the dependencies.

The first step is the same - we need to clone the repository, which will create the directory “reforge” in your current directory and download the GitHub repository.

git clone https://github.com/DanYev/reforge.git

Go to the downloaded directory, start a session with enough memory, and run the installation script:

cd reforge
interactive --mem 16G
. scripts/installation_phx_sol.sh

If the above fails, try requesting more memory, remove the environment, and start over:

source deactivate
mamba env list
mamba remove -n reforge --all

If the installation was successful, restart the shell (or quit the interactive session by typing exit) and run the tests. You can find the log in tests/sl_output.out

cd reforge
. scripts/phx_md_load.sh # on PHX
. scripts/sol_md_load.sh # on SOL
sbatch run_tests.sh --all

If the above does not work for you, or some of the tests fail, email me at dyangali@asu.edu