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
- Adding a Residue to a Force Field
- Water solvation
- Non water solvent
- Mixed solvent
- Making Disulfide Bonds
- Running membrane simulations in GROMACS
- Parameterization of novel molecules
- Potential of Mean Force
- Single-Point Energy
- Carbon Nanotube
- Visualization Software
- Extracting Trajectory Information
- External tools to perform trajectory analysis
- Plotting Data
- Micelle Clustering