GROMACS version: 2021.4
GROMACS modification: No
I am working on a project related to water desalination through nanoporous membranes. I have been trying to set up a system with a nanoporous membrane in the middle of the box and two graphene sheets at the end faces. To achieve this, I utilized CHARMM-GUI to generate a MoS2 membrane using the Interface force field. Subsequently, I employed a Python script to introduce a nanopore into the membrane by editing the PDB file. For manipulating the structure, I utilized MD Analysis to define a cylindrical zone within the membrane, deleting the atoms within this zone, and saving the modified structure into a new PDB file. My current challenge lies in generating the itp (topology) file necessary for the modified structure. Despite attempts using Parmed and MDAnalysis, I have encountered difficulties in this process. I have experience in simulating biophysical systems and this is the first time I am dealing with a nanomaterial system. So I am not very sure if I am approaching this in a correct or reasonable way. I would greatly appreciate any suggestions you could offer to steer me in the right direction.