I am workin with deposition and I am trying to run TAD (Temperatura Accelerated Dynamics). This is because after each deposition I want to know if a have a long term diffusion.
My doubt is: If I run tad with boundary conditions "ppm" I have problems of different atoms number or different bonds number between replicas. I have tried to minimize the system before running tad, but it didn't help.
If I run tad with "ppp", everything is ok. But my system is not ppp, I have a surface!