I have a system of MICELLE in water.
In order to generate MICELLE I used MATLAB script to force the monomers to take a shape close to spherical micelle and then using appropriate parameters between same species like water-water, hydrophilic-hydrophilic parts of monomer, hydrophobic-hydrophobic parts of monomer and between different species like water-hydrophilic part of monomer, hydrophilic-hydrophobic parts of monomer (all monomers together form Micelle) to have monomer assembled by running a simulation.
The micelle at the end of the simulation remains assembled with the above mentioned parameters From VMD i can see that the micelle is assembled and hydrophilic part of the micelle faces water and hydrophobic part makes the core of the micelle and I can see brownian motion of the micelle…
I wanted to be sure that I have the perfect micelle and I want to calculate the DENSITY PROFILE of the micelle, but the available compute and fix
COMPUTE id GROUP-ID chunk/atom bin/1d x 0 0.1
fix fix-id hydrophobic_part ave/chunk 1 10 1000 id density/number norm sample file densityhydrophobic.profile
will not give me what I want.
Can anyone tell me how I can calculate the density profile of MICELLE to be sure that there is no problem with the assembly of micelle?
INP TOULOUSE FRANCE