periodic BC for molecular dynamics

[amitwsu]

How do we apply periodic boundary condition in Molecular Dynamics calculation.  If applied, the atom leaving the box from one end should appear at the opposite end.  I see in my MD simulation that the atoms are leaving the box and stay outside the box.

Thanks
Amit

[Jess Wellendorff]

You will probably need to use a BulkConfiguration for your system, not a MoleculeConfiguration. Do you use BulkConfiguration?

[Anders Blom]

If you see a box, it means the system is already a BulkConfiguration. In this case, periodic boundary conditions always apply and your calculation is correct even if the atoms appear to leave the cell; in the computation they are wrapped.

In the 2016 version of ATK, there is an option in the Movie Tool to automatically wrap the atoms inside the cell when looking at the movie, but from a physical perspective it's more correct that the atom leaves the cell, if you e.g. want to calculate the diffusion rate you need the actual distance traveled, without wrapping.

Please always state your version of ATK/VNL when asking these kinds of questions, as the behavior may be different in different versions.