Distance between water molecules and residues

GROMACS version: 2021.3
GROMACS modification: No
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I am looking into aggregation of surfactant molecules into micelles. At low surfactant concentration, the entire surfactant is hydrated but as the concentration increases, aggregation occurs which results in formation of spherical micelles. The hydrophobic part of the surfactant forms the core while hydrophilic part forms the corona. This is accompanied by dehydration of the hydrophobic part to enable better packing of the core while the hydrophilic part dehydrates due to denser packing in the corona.

My question is: is there a way to follow the dehydration process throughout the trajectory frames? I am not sure but maybe something akin to the distance between the COM of a residue of the polymeric surfactant and the nearest water molecules. Or, any other better approach?


Hi @rpsingh,

my suggestion would be a radial (or cumulative) distribution function (RDF/CDF). You could split your trajectory in multiple parts and calculate for each part the RDF/CDF. However, this is only one possibility to show the dehydration process.