I am not an expert of the Gromacs. However, I will share a related reference to you!!

Omkar S. Kushwaha

thank you for every thing .

I usually create snapshots of the simulations that can be opened in VMD (https://www.ks.uiuc.edu/Research/vmd/)

Later in VMD you can make the calculation for counting the molecules inside the CNT; it uses the TCL language which is a bit strange at the beginning.

(https://www.ks.uiuc.edu/Research/vmd/)

You can find each molecule in .gro file with coordination (x,y,z) for instance your CNT has a special coordinate that helps you to limit the number of water molecules in CNT. Usually, the number of water molecules are very much and you can not do this method manually. I use MATLAB with a loop (for and if) that analyzes coordinates of water molecules with special limits.

Berezhkovskii, Alexander, and Gerhard Hummer. "Single-file transport of water molecules through a carbon nanotube." Physical review letters 89, no. 6 (2002): 064503.

Yamamoto, Eiji, and Kenji Yasuoka. "Water molecules in a carbon nanotube under an applied electric field at various temperatures and pressures." Water 9, no. 7 (2017): 473.