Installation

Prerequisites

  1. A working version of conda/miniconda

  2. A working version of git

  3. A CUDA - capable device (locally or node). A CUDA device is not required to generate the intermediate states, but one is required to do simulations or analyses.

Getting \(\texttt{TRANSFORMATO}\)

First, install conda on your machine. Then clone the repository

git clone https://github.com/wiederm/transformato.git

Within the newly created transformato directory, a yaml file can be found in devtools/conda-envs/. Use conda to create an environment called fep by going into the transformato directory and using conda:

cd transformato
conda env create --file devtools/conda-envs/fep_env.yaml

Caution

If you are doing this the first time, this may take a while (up to 10 minutes!)

Activate the environment with conda activate fep.

Note

For running simulations on an NVIDIA machine using CUDA, openMM will install the python package cudatoolkit. Make sure the version in your environment is not higher than the CUDA version of your NVIDIA driver (you can check by using nvidia-smi for the driver and by conda list you can see your current version). If necessary, you can install the correct cudatoolkit version by using conda install cudatoolkit=X.Y -c conda-forge

Now install \(\texttt{TRANSFORMATO}\) with:

python setup.py install

This will install \(\texttt{TRANSFORMATO}\) in your current (fep) conda environment.

Now, you can open python try the following command:

import transformato
print(transformato.__version__)

If you output the current transformato version, then congratulations! You are now ready to use transformato.