The High throughput binding affinity calculator (HTBAC) is a scalable solution for adaptive personalised drug discovery. HTBAC it uses high level python object abstractions for defining simulations, physical systems and ensemble-based free energy protocols. The Runner class as part of the HTBAC abstraction uses underlying building blocks middleware developed by the RADICAL team to create and execute multiple concurrent executions of protocols on supercomputing cyberinfrastructures while abstracting and handling execution management, and data transfer.