This project uses the lammps_multistate_rods library to make coarse-grained multi-scale hybrid MD-MC simulations of amyloidogenesis.
The project is written in python3 and contains scipts and programs to set up everything for the simulations, submit them as jobs on remote clusters and exctract, analyse and visualise the data from those simulations.
Study the scripts in the setup_scripts folder, that should be enough.
The requirements are:
-
Python 3 (min 3.5, it's NOT Python2 compatible) with mpi4py and matplotlib (for analysis tools), along with libraries needed for the lammps_multistate_rods library:
pip install mpi4py matplotlib ... -
Jupyter (or equivalent to run IPython notebooks) is necessary to run the analysis notebooks
- The following terminal line can be of use to enable Jupyter to use a venv kernel that has everything installed (presumably the system python won't be used):
python -m ipykernel install --user --name=<kernel-name>Then that kernel can be chosen in Jupyter/IPython to run the code (menu under "Kernel").