Sometimes you may want to output your setup and simulation results in another place. This can happen on clusters and shared directories where there may be a common repository of directories where the YAML script lives, but the work directory or drive is located elsewhere.
This recipe manipulates the output directories for a YANK setup and simulation. Normally, the default options are chosen and these don't have to be set.
There are two flavors here. The first assumes the YAML script is in a directory which can be written to and has the space to store the YANK experiments. The second is a very uncommon recipe where a central molecule setup directory is used. This is extremely uncommon but for similar experiments may be helpful. Because the default settings of these options exist, in most cases, you will likely never use these recipes.
Note
The output_dir path is relative to the YAML file location, but the other paths are relative to
output_dir Keep this in mind when setting paths.
Absolute paths, however, are always respected.
.. literalinclude:: raw_cooking_basics/rawpathscommon.yaml :language: yaml
.. literalinclude:: raw_cooking_basics/rawpathsrare.yaml :language: yaml