I have generated successfully an initial configuration of PE in a 50x50x50 A^3 box.
However, once in LAMMPS, I am interested in studying the interaction of this polymer with a wall. In order to do so, I modify the data file:
0 50 xlo xhi
0 50 ylo yhi
-10 50 zlo zhi <------
The problem I face is that since Polymer Modeler considers periodic boundaries, when I modify the zlo value I obtain long bonds.
How could I solve this issue? Somebody has generated an initial configuration and used it in a larger simulation box?
I will appreciate your help.