It is a bit hard to say what particular physics/biological processes do you want to model, so I will give a more general recommendation:
Wiki page on software for molecular mechanics modeling
In particular, I would point you to LAMMPS that is suited for distributed systems and is very popular.
What about software-as-a-service offers? With https://www.circuitlab.com/ you can run simulations in your Browser. It is commercial software, subscription-based.
I don't know how well this can scale up. Maybe the web can handle only simple circuits.