Dear altruists, I am a beginner in molecular dynamics simulation using Lammps. I am trying to simulate a selective ion/particle water filter using carbon nanotubes.

I have built the system using Moltemplate and run it in NVT using Lammps and using vmd and Ovito as a visualizing tool.

But I am failing to... 1. apply pressure on the water box exclusively (along the tube axis). 2. change the chirality of the nanotube in moltemplate. (the pdb file obtained from vmd's nanotube builder is facing issues when being converted to moltemplate file; that's why have to put a lot of atoms manually)

3. a good method to compute the velocity of water molecules within the nanotube

Any suggestions regarding these or learning Lammps will be of great help. Thank you in advance