To analyze protein-ligand interactions during the course of a simulation you can use the “Analyze Trajectory…” protocol. To do this analysis follow these steps:

1. Make sure the ligand is defined in the Receptor-Ligand Interaction Toolbar under View Interactions.
2. In the Menu Bar select Structure > Monitor > Non-bond interactions and select which interactions to monitor. Make sure Intermolecular is selected.
3. Open the “Analyze Trajectory…” protocol which is located in the Simulation Toolbar under Analyze trajectory.
4. In the protocol, under Analysis type select Properties. Under Properties, you should see the previously created monitor (e.g. Non-bond Monitor 1).

Part of the results is a plot with the frequency of the interactions, which may prove useful to visualize the prevalence of the interactions.