In Martini, while modelling Protein-membrane system, water density doesn’t match real water (≈1000 kg/m³) but instead looks artificially high, often around 2000 kg/m³.
Is this a consequence of coarse-graining mapping (4 water:1 bead) where martini is parameterized to reproduce thermodynamic properties, and not to match the exact density of water in real units? Please help me to understand this.
Thank you in advance.
I'm no expert on Martini, but you could take a look at page 47 of the supplementary information in this paper:
Article Martini 3: a general purpose force field for coarse-grained ...
According to this, the mass values are chosen for simplicity and numerical stability rather than to reflect realistic masses. If you're interested in thermodynamics, this is fine, as mass values don't matter. However, if you're interested in kinetics, you might want to consider carefully, as the paper points out.
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