NVE Simulation with one Non-periodic Boundary

LAMMPS LAMMPS General Discussion
1

Hello Dr. Akohlmey:

I’m working with a bulk system in the presence of a surface. I have periodic boundary condition along x, y and fixed boundary along z. I’m using “fix setfoce” command to make the silica surface and the hydrophobic surface immobile. The bulk is in contact with the surface via silanol group. The hydrogen is free to move in a cone. There is enough distance between liquid and hydrophobic surface to accommodate the vapor saturation surface.

Attempting NVE simulation, I have notice that there is an increase in temperature and as a result the kinetic energy. To check where the issue comes from (aside from time step), I did a bulk NVE simulation and there was no increase in energy. This mean the bulk has no issue.

In the second try, I froze the hydrogen of the surface and in this case the temperature/kinetic energy is increasing slowly. This behavior makes me think that the non-periodicity along z-axis and the lack of image molecule is making the time integration to accumulate the error faster so that energy is increasing slowly.

Is this explanation correct? If not, could you guide me in the correct direction!

Thanks
Shah

2

No.

It is difficult to make any statement based on your rather vague description. I would speculate that you see different levels of reconstruction and that is more a question of how you equilibrate your initial geometries.

The only factor that affects the time integration is the time step. Thus if time integration is the problem, the issue should go away when you reduce the time step. Since you mention hydrogen atoms, there could be a problem with hydrogen atoms altogether since they require a shorter time step compared to heavier atoms due to their much lower weight. This would go away if you freeze them. But lack of equilibration is the more likely issue.