Software Requirements

Python

Our scripts are tested on python versions 3.4 - 3.6. We recommend downloading and installing anaconda, which ships with most of the heavily used modules in LLC_Membranes.

Some modules that you may need to install manually include:

• mdtraj
• tqdm
• ruptures
• fbm

All are available on PyPI and can therefore be installed using pip.

GROMACS

Most of the python packages in LLC_Membranes have been tested on trajectories and coordinate files generated using GROMACS version 2018.3. The scripts should work with any version of GROMACS greater than or equal to 5.x (when the all tools became modules of a binary names gmx).

See their documentation for Installation instructions.

AmberTools

We parameterize monomers and solutes using the generalized amber force field (GAFF). One can parameterize organic molecules with GAFF using the antechamber package which comes with AmberTools.

See their download page to obtain the software for you machine.