This website is a resource aimed at researchers from the BioKT lab to have working examples of different types of molecular dynamics simulations that can be run using Gromacs patched with PLUMED. These examples borrow extensively from the fantastic PLUMED masterclasses, but are necessarily less exhaustive and intended to provide working examples of methods we routinely employ.
- Umbrella sampling
- Metadynamics
- Simulations with multiple replicas