GROMACS version: 2020.5
GROMACS modification: No
I am trying to perform a simulation with a graphite structure in the middle of the box (5 stacked graphene layers), something like a membrane. To make the graphite infinite in the x-axis in using the “periodic-molecules = yes” option in the mdp file. However, when I run the minimization energy step seen that the graphene layers are not coupling with their periodic images in the x-axis.
To ensure that the layers are coupling to each other I just have to guarantee that the PBC atoms are within the “bond” distance of the atoms from the original box? Or there is something that I should add to the ITP file? Does anyone have any tips or advice?
I am attaching a picture of the layers with the PBC before and after the minimization.
Thank you !