BioSimSpace.Metadynamics.CollectiveVariable.viewFunnel(system, collective_variable, property_map={})[source]#

Visualise the shape of the funnel defined by the collective variable. This is useful for checking that the funnel configuration is sane prior to running any metadynamics simulations. The function returns a BioSimSpace.Notebook.View object, allowing the user to customise the visulisation.

  • system (System) – The system of interest. This is assumed to be a solvated protein-ligand system.

  • collective_variable (Funnel) – The funnel collective variable.

  • property_map (dict) – A dictionary that maps system “properties” to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { “charge” : “my-charge” }


view – A view object showing the system and funnel.

Return type: