I ran it a couple of times for different box dimensions, but changing the box dimensions did not have an effect, it flags an error of bond atoms missing.
I don’t think that will make a difference.
You get the “atoms missing” error when atoms leave the simulation box. There are multiple possible reasons for that. Close contacts (and thus moving too fast during MD) and atoms being able to leave the box with fixed boundaries are the most common reasons. Close contacts are quite possible in your setup due to random placement of atoms with create_atoms you would have to delete overlapping atoms or use one of multiple possible “unoverlapping” strategies. The most convenient way to do this is currently only available, if you compile the latest development branch from source from the LAMMPS git repository, where you can check for overlaps during atom/molecule creation and retry in a different location. The most likely reason in your input is the fact that you do not properly immobilize your substrate atoms. Adding:
group mobile subtract all substrate substrate2
and then applying time integration and thermalization only to the mobile group should help with that.
You get “bond atom missing” errors for similar reasons. Applying minimization may not be sufficient to resolve overlaps. For as long as you have only one large molecule to place, i would use create_atoms single instead of create_atoms random and thus make certain that you place the molecule at a place away from all possible overlaps. You can still have random orientations.
Thank you so much, I will positively look into all possible remarks.
I wanted to clarify that in actuality, I do not have a single polymer to be deposited on the charged substrate, I have around 30 polymers to be deposited on the substrate could recommend alternative options to deposit multiple polymers? I wanted also to inform you that adding the group excluding the substrate yet flagged an error for missing bond atoms. I would value your remarks on this
I have nothing to add to what I already explained.
20_05_2022.txt (4.0 KB)
I changed the insertions from distributing the ions randomly across the box to inserting only in certain regions. I was able to get the PE on the charged substrate. I stratified the regions for PE, counterions and co ions for neutralising the substrate.