Short How-To guides

A number of short guides are presented here to help users getting started with simulations. Useful third-party tutorials provided by Justin Lemkul are found here http://www.mdtutorials.com/.

• Beginners
  • Resources
• Adding a Residue to a Force Field
  • Adding a new residue
  • Modifying a force field
• Water solvation
• Non water solvent
  • Making a non-aqueous solvent box
• Mixed solvent
• Making Disulfide Bonds
• Running membrane simulations in GROMACS
  • Running Membrane Simulations
  • Adding waters with genbox
  • External material
• Parameterization of novel molecules
  • Exotic Species
• Potential of Mean Force
• Single-Point Energy
• Carbon Nanotube
  • Robert Johnson’s Tips
  • Andrea Minoia’s tutorial
• Visualization Software
  • Topology bonds vs Rendered bonds
• Extracting Trajectory Information
• External tools to perform trajectory analysis
• Plotting Data
  • Software
• Micelle Clustering