Martini versus Charmm
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- Last Updated: Monday, 27 June 2022 11:48
From the Risselada lab: a comparison between Martini 2, 3, and Charmm36 on the binding of amphipathic peptides to lipid bilayers. From the abstract: "We observed that Martini 3 qualitatively reproduces experimental trends while producing substantially lower (relative) binding free energies and shallower membrane insertion depths compared to atomistic simulations. In contrast, Martini 2 tends to overestimate (relative) binding free energies." For more details, see: van Hilten et al., JCTC 2022.
The group of Basdevant performed Martini simulations of the ionic transport through the α-hemolysin protein nanopore, using the polarizable water model. The electric potential difference applied experimentally was mimicked by the application of an electric field to the system. They were able to observe current asymmetry and anion selectivity, in agreement with previous studies and experiments, and identified the charged amino acids responsible for these current behaviors.
Simulations with Martini 3 reveal how lipids unplug pyroptotic pores formed by gasdermin-A3.