List of the main repos and databases we develop and contribute to.
Check out also our Group Github repo.
Martini 3 Small Molecule Database
A dataset of Martini 3 coarse-grained models of small molecules.
[GitHub repo]
Polyply
A software package, written in Python, to facilitate the simulation of macromolecules and other complex systems.
[GitHub repo]
PySAGES
A software package, written in Python, that implements advanced sampling methods and that runs on GPUs.
[GitHub repo]
Bartender
A software package, written in Go, for automated and QM-based parametrization of Martini 3 bonded terms.
[GitHub repo]
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Martini 3 Small Molecule Database
Dataset of coarse-grained models
Key publication(s):
Alessandri, Barnoud, et al., Adv. Theory Simul. 2022 [link]
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Polyply
High-throughput simulation software
Key publication(s):
Grünewald, Alessandri, et al., Nat. Commun. 2022 [link] [GitHub repo]
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PySAGES
Enhanced sampling on GPUs
Key publication(s):
Zubieta Rico, et al., npj. Comput. Mater. 2024 [link] [GitHub repo]
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Bartender
QM-based Martini bonded parametrization
Key publication(s):
Pereira, Alessandri, et al., JCTC 2024 [link] [GitHub repo]