I am trying to simulate a graphite sheet in vacuum. I am following below gromacs link for simulating carbon nanotubes for that.
I made the initial pdb of graphite using VMD nanotube builder utility. I followed exact steps of the tutorial.
However I am not sure if my graphite is periodic.
Q. How to check if the sheet is a periodic inifinite sheet.
Q. Periodic molecules are infinite molecules like sheets, nanotubes, etc. that have bonds between central image atoms and periodic copies of atoms. (Link: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-August/121676.html)
How to provide these interactions between central image and periodic copies of atoms.
Q. Does one has to semiisotropic pressure coupling for maintaining periodicity. Does box parameter here have to be correlated to lattice parameters of sheet?
Thanks in advance.