Preparation

• 2. Prepare a directory for a NEMAT run: nemat start
• 3. Prepare the membrane-embedded protein (MEP) system.
  • 3.1. Creating the MEP system using CHARMM-GUI.
  • 3.2. Using a different method.
• 4. Prepare the membrane system.
  • 4.1. Create the membrane system using CHARMM-GUI.
  • 4.2. Using a different method.
• 5. Prepare the ligands.
  • 5.1. Obtaining the reference ligand: ref_lig.pdb.
  • 5.2. Obtaining the membrane reference ligand: ref_lig_mem.pdb (optional).
  • 5.2. Aligning the ligands.
• 6. About the mdp files
• 7. Set up of NEMAT: the input.yaml file
  • 7.1. Job script setup.
  • 7.2. Production and Transitions setup.
  • 7.3. Analysis setup.