Melting Metallic Particles on Graphene

Please reply to the mailing list, not to me.

If you want to know how to do it, you should check the available literature. However, you started by saying you had a setup that worked but now produces inconsistent results. Maybe you want to figure out why that is instead? What you are describing now sounds like unstable dynamics, so either your initial setup is bad or your time step is too large.