Quickstart (for the impatient)

First, install the anaconda scientific Python distribution.

Install the release version of YANK from the omnia Anaconda Cloud channel (check out our detailed installation section):

$ conda install -c omnia yank

Go to the examples/p-xylene-implicit directory to find an example of computing the binding affinity of p-xylene to T4 lysozyme L99A:

$ cd ~/anaconda/share/yank/examples/p-xylene-implicit

Run an alchemical free energy calculation (in serial mode) using the parameters specified in the yank.yaml file:

$ yank script --yaml=yank.yaml

Alternatively, the simulation can be run in MPI mode if you have multiple GPUs available.

Analyze the simulation data:

$ yank analyze --store=experiments