How-to
Simulations
- List of servers
- How to submit jobs to clusters
- How to prepare a system
- How to parameterise ligands
- How to run rosetta ab initio modeling
- How to do dockings
- How to do MDs
- How to do Targeted MD
- How to do enhanced sampling
- How to do umbrella sampling
- How to do free energy perturbation
Analysis
- How to use some common python packages
- How to do RMSD and RMSF
- How to do clustering of trajectories
- How to do covariance analysis
- How to do geometrical analysis
- How to do HOLE analysis
- How to do Direct Coupling Analysis
