# Examples for YANK

## Very fast, simple examples
* `benzene-toluene-implicit/` - benzene and toluene in implicit solvent
* `benzene-toluene-explicit/` - benzene and toluene in explicit solvent
* `host-guest-implicit/` - host-guest association in implicit solvent
* `host-guest-explicit/` - host-guest association in explicit solvent
* `tip3p-in-tip3p/` - TIP3P water in TIP3P explicit solvent

## Standard size examples
* `p-xylene-implicit/` - p-xylene binding to T4 lysozyme L99A in implicit solvent
* `p-xylene-explicit/` - p-xylene binding to T4 lysozyme L99A in explicit solvent
* `p-xylene-gromacs-example/` - p-xylene binding to T4 lysozyme L99A in explicit solvent using gromacs input files

## Larger, more complex examples
* `nacl-explicit/` - Na+ and Cl- association in explicit solvent
* `mhc-peptide-tcr/` - alchemically eliminate a peptide binding at the interface of an MHC and TCR, illustrating use of Yank Python API for system setup
* `abl-imatinib-implicit/` - Abl binding to imatinib in implicit solvent
* `abl-imatinib-explicit/` - Abl binding to imatinib in explicit solvent
