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Metastability is one of the major encountered obstacle when performing longmolecular dynamics simulations, and many methods were developed to address thischallenge. The "Parallel Replica" (ParRep) dynamics is known for allowing tosimulate very long trajectories of metastable Langevin dynamics in thematerials science community, but it relies on assumptions that can hardly betransposed to the world of biochemical simulations. The later developed"Generalized ParRep" variant solves those issues, but it was not applied tosignificant systems of interest so far.  In this article, we present the program gen.parRep, the first publiclyavailable implementation of the Generalized Parallel Replica method (BSD3-Clause license), targeting frequently encountered metastable biochemicalsystems, such as conformational equilibria or dissociation of protein-ligandcomplexes. It will be shown that the resulting C++ implementation exhibits astrong linear scalability, providing up to 70 % of the maximum possible speedupon several hundreds of CPUs.

gen.parRep: a first implementation of the Generalized Parallel Replica dynamics for the long time simulation of metastable biochemical systems