Periodicity of graphite sheet in MD simulation

[Pragati]

Dear all,

I am trying to simulate a graphite sheet in vacuum. I am following below gromacs link for simulating carbon nanotubes for that.
“http://www.gromacs.org/Documentation_of_outdated_versions/How-tos/Carbon_Nanotube”

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.

[alevilla]

Hi
below some answers

@Pragati

Dear all,

I am trying to simulate a graphite sheet in vacuum. I am following below gromacs link for simulating carbon nanotubes for that.
“http://www.gromacs.org/Documentation_of_outdated_versions/How-tos/Carbon_Nanotube”

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.

you can visualize in VMD using the option graphics → representations → periodic

Then be sure, that you simulate using pbc option in mdp file (see http://manual.gromacs.org/current/user-guide/mdp-options.html?highlight=pbc#mdp-pbc)

Q. Periodic molecules are infinite molecules like sheets, nanotubes, etc. that have bonds between central image atoms and periodic copies of atoms. (Link: [gmx-users] periodic-molecules = yes and movie)

How to provide these interactions between central image and periodic copies of atoms.

to have a periodic molecules add the option periodic-molecules = yes to mdp file (Note the bond should be properly defined in the topology)

Q. Does one has to semiisotropic pressure coupling for maintaining periodicity. Does box parameter here have to be correlated to lattice parameters of sheet?

do you plan to simulate in vacuum? why do you want pressure coupling? what about NVT?

Thanks in advance.

Kind regards
Alessandra