Alchemical Networks: Planning a Simulation Campaign#
The goal of the setup stage is to create an AlchemicalNetwork,
which contains all the information needed for a campaign of simulations.
This section will describe the composition of the achemical network,
including the OpenFE objects that define chemistry, as well as
alchemical transformations.
Like any network, the AlchemicalNetwork can be described in terms
of nodes and edges between nodes. The nodes are ChemicalSystems,
which describe the specific molecules involved. The edges are
Transformation objects, which carry all the information about how
the simulation is to be performed.
In practice, nodes must be associated with a transformation in order to be relevant in an alchemical network; that is, there are no disconnected nodes. This means that the alchemical network can be fully described by just the edges (which contain information on the nodes they connect). Note that this does not mean that the entire network must be fully connected – just that there are no solitary nodes.
Each Transformation represents everything that is needed to
calculate the free energy differences between the two
ChemicalSystems that are the nodes for that edge. In addition to
containing the information for each ChemicalSystem, the
Transformation also contains a Protocol and, when
relevant, atom mapping information for alchemical transformations. The latter
is often done through a LigandNetwork.
