Computing free energies of fold-switching proteins using MELD x MD

In this Zenodo repository, we provide the MELD script and data for a few representative systems in the DP-MELD.zip, GA_GB-MELD.zip, and RfaH-MELD.zip files. The contents of the repository are described below:

1. MELD Simulation:

   • Filename: DP-MELD.zip, GA_GB-MELD.zip, and RfaH-MELD.zip
   • Description: These archives contain the necessary files and scripts for the MELD simulation.

2. Setup Script:

   • Filename: setup.py
   • Description: This script is used to set up the MELD simulation.

3. Trajectory Analysis Script:

   • Filename: Clustering.sh
   • Description: This script analyzes the trajectories obtained from the MELD simulation.

4. Protein Information:

   • Location: TEMPLATES folder
   • Files:
     • Protein topology file: .top
     • Coordinate file: .crd
     • PDB file: .PDB
   • Description: These files provide input information for a few representative proteins.

5. Residue-Residue Contact Information:

   • Files:
     • contact_model1.dat
     • contact_model2.dat
   • Description: These files contain information about the contacts between residues.

6. Replica Trajectory Files:

   • Filename: trajectory.00.dcd
   • Description: These files contain the trajectories obtained from the simulation for the corresponding bottom replica.
7. Clustering Output:
   • Folders: Cluster_6 or Cluster_3.5
   • Description: These folders contain the results of the clustering analysis, including the computed population and the average conformers for each cluster.

Furthermore, we provide an additional archive called unfold.zip:

1. Unfolded Ensemble:
   • Filename: unfold.zip
   • Description: This archive contains the unfolded ensemble, which is used to determine the force required for rebalancing two group springs for the MELD run between two conformers (A and B) before executing the MELD simulation.