I think the polarization here only refers to orientation of the dipole moment vectors. So, the author has basically calculated the distribution of the magnitude and y-component of these vectors for the two water layers.

Dear Roja

- After MD simulation, you can see water molecules around surface (as attached, Here, for water mulecules around nano tube).

- You have to write a code to tranfer each water moelcule (1 oxygen + 2 hydrogen atom) to a dipole vector (dipole vector, as shown in another photo attached here).

- Then you need to add another section to your code to analyze the dipole vectors.

- In order to calculate the distribution and number of water molecules in RADIAL distance around amino acid, you have two choices : 1- use available MD analysis softwares such as WMD, OVITO and .... 2- write your own code.

I suggest you read this paper:

"Structural properties of water around uncharged and charged carbon nanotubes"

Korean J. Chem. Eng., 30(3), 693-699 (2013) DOI: 10.1007/s11814-012-0198-6

Let me know if you have any question.

Check out order parameter. That's the most common way of quantifying orientation. Once you convert each water molecule into a dipole vector as mentioned by @Amir, you can calculate the angle and then order parameter.

For radial distribution, you can use VMD or write a code. I'd suggest you write a code for everything.

Thank you so much for your detailed answer.

Dear Amir Reza Ansari Dezfoli , i've read the article. it was really helpful. Since, i've not used TINKER, did you write a code for all your analysis, or they are embedded in TINKER by default?

Best

Dear Roja Rahmani

Thanks for positive feedback. Actually, I wrote a code in MATLAB. For MD simulation, I strongly suggest LAMMPS code package (Free, used friendly and you can calculate RDF (Radial distribution function) easily).

If you decide to write a code and/or you have any question, let me know

Thank you so much Amir Reza Ansari Dezfoli , i use GROMACS and i've not write a code, are you familiar with GROMACS tools?

However i like to write my own code, also.

and i have a question about fig.2 in the article. does it potential mean force(PMF) you calculated from umbrella sampling?

Roja Rahmani

Figure 2 in my article is total energy between a water molecule and a carbon nano tube when water molecules has different orientation toward nano tube.

I'm not familiar with GROMACS, I've worked with TINKER, GULP and LAMMPS.