VMD-L Mailing List

From: sheikh sameer (sheikhsameer229_at_gmail.com)
Date: Fri Oct 08 2021 - 09:55:58 CDT

Hello Everyone,

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?

Thanks
Sheikh Salahudin
PhD Student
INP TOULOUSE FRANCE