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In the long Wikipedia list of simulation environments I find only a CFD simulation for cloud.

Which would you use for molecular biology simulations with cloud computing?

Criteria: it should be possible to reproduce the polio virus simulation from 2014.

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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:

In particular, I would point you to LAMMPS that is suited for distributed systems and is very popular.

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