VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Oct 08 2021 - 11:05:29 CDT

Please try not to be sloppy here: you're pasting commands from another
package (in this case LAMMPS) assuming that every person on the VMD mailing
list will know what those commands mean. And if you don't bother to
explain what's the problem with those commands, what good does it do to
include them?

For a radial density profile, if you want to do this outside LAMMPS because
e.g. you're post-processing, basically you're going to need to compute the
center of mass of the micelle (taking care that PBC wrapping does not
interfere with the computation) and then transform all Cartesian
coordinates of the micelle atoms into spherical ones, or at least compute
just the radial coordinate, r. At that point you just compute a histogram
of r weighted by whatever you're using.

Don't know what's a "perfect micelle" (some of them have funny shapes and
they're just fine like that). If you are looking for a 3D density map you
could use the volmap command in VMD or the corresponding GUI:
https://www.ks.uiuc.edu/Research/vmd/plugins/volmapgui/
Again, you need to center the micelle on a fixed position (e.g. the origin)
and make sure PBC wrapping is not an issue. If you don't know what that
means, please read about those two first.

Giacomo

On Fri, Oct 8, 2021 at 11:34 AM sheikh sameer <sheikhsameer229_at_gmail.com>
wrote:

> 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
>