I am simulating a lattice and using periodic boundary conditions in x and y and fixed boundary condition in z direction. I have also considered making my simulation cell a bit larger in z-direction to give the atoms some room to vibrate. But still I find atoms get lost .
I first equilibrated the sample my using NPT ensemble as shown:
fix 4 all npt temp 1000 1000 1.0 x 0.0 0.0 1.0 y 0.0 0.0 1.0 couple xy
run 50000
During equilibration no atoms lost
Then heating the sample from 1000K to 3500 K using NPT as :
fix 5 all npt temp 1000 3500 1.0 x 0.0 0.0 100.0 y 0.0 0.0 100.0 couple xy
run 1000000
Time step is 0.5 fms