This repo contains python scripts used in Khella et al. 2023 (doi.org/10.1016/j.jbc.2023.104796). This includes MD simulations code and analysis scripts. The usage of these Python scripts is further explained in the enclosed README.pdf
The MD simulation production and analysis scripts were designed for ubuntu based NVIDIA GPU servers using the cuda toolkit (Version 12). Visit
for installation instructions.
After installation, check for the correct set up by running
nvidia-smi
in your terminal.
The output should state the CUDA Version and driver version as displayed below
Best way to install packages is by using conda. Either install the full anaconda distribution (https://www.anaconda.com/) or the smaller footprint miniconda (https://docs.conda.io/en/latest/miniconda.html).
create a new conda environment (here named 'sim') by running
conde create -n sim
install the necessary packages by running
conda install conda-forge::openmm
conda install conda-forge::mdtraj
conda install conda-forge::pdbfixer
conda install -c conda-forge contact_map
conda install anaconda::openpyxl
For the underlying MD data in the publication go to doi.org/10.18419/darus-3263.
Please cite doi.org/10.18419/darus-3263 for the usage of this dataset.
Please cite doi.org/10.1016/j.jbc.2023.10479 for the publication.