This repository contains necessary information to reproduce the molecular dynamics simulations presented in this paper.
This work is the MD portion associated with A learnable transition from low temperature to high temperature proteins with neural machine translation TODO LINK
- All simulations were performed using GROMACS 2022.5 compiled on The University of Washington Hyak computer cluster.
- The structures provided are solvated and energy-minimized.
- Generic
.mdp
files used to simulate all replicas for every protein. rmsd.py
is an example script that calculates the RMSD of an ensemble of protein structures at different temperaturesrmsd_pkls.zip
contains pickle files of rmsd values calcualted for all simulationsMD-figs.ipynb
is the notebook used to read the pkl files and create the MD figure in the manuscript.