chrispy67 / nomelt_md

Molecular dynamics SI for nomelt proejct

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 temperatures
• rmsd_pkls.zip contains pickle files of rmsd values calcualted for all simulations
• MD-figs.ipynb is the notebook used to read the pkl files and create the MD figure in the manuscript.