Installation

PyMEMENTO can be installed either from the PyPI repository or from the github source code. It is recommended that you do this in a fresh conda environment:

conda create -n PyMEMENTO python=3.9
conda activate PyMEMENTO

PyPI installation

PyMEMENTO is pip-installable, therefore the latest release can be installed with:

pip install PyMEMENTO

Installation from source

Alternatively, you may install the latest version using the source code on github.

git clone https://github.com/simonlichtinger/PyMEMENTO.git
cd PyMEMENTO
pip install .

Additional packages

PyMEMENTO depends on other packages that require some manual setup.

• Modeller

  For template-based modelling, PyMEMENTO relies on modeller developed by the Sali lab. The package is available on conda (conda install -c salilab modeller), but requires a license to run and cannot be bundled into separate projects. Please obtain a license here and follow the installation instructions. PyMEMENTO checks for a correct modeller installation and will raise a warning if none is found.

• Gromacs

  PyMEMENTO runs solvation of boxes and energy minimizations via the gromacs MD engine. You can install it using the instructions. Alternatively, you can use a pre-compiled binary available on conda (conda install -c bioconda gromacs=2021.3), which may be slower for running MD but will do the job for PyMEMENTO. PyMEMENTO checks for a correct gromacs installation and will raise a warning if none is found.

• Plumed

  If you wish to use PyMEMENTO to set up umbrella sampling for your equilibrated boxes, you will need to install plumed. This can be done using their instructions or the conda package (conda install -c conda-forge plumed). A version of gromacs patched with plumed is not required to run this package, but is essential for running the subsequent umbrella sampling. PyMEMENTO checks for a correct plumed installation and will raise a warning if none is found.