I am facing a problem concerning the generation of a polymer melt and its use in LAMMPS. Maybe some of you have experience in this.
I can generate a polymer melt inside a box of periodic boundaries by means of Polymer Modeler of www.nanohub.org. However, when I change the simulation box dimensions in the data file in order to give space for the wall atoms I find out that the bonds that spaned the walls become very large according to the new simulation box. This leads to unphysical results and crashes.
The question is the following: How could I generate a polymer melt not inside a box of periodic boundaries but inside a “real” box? This way, no bond would span the boundaries and I could change the simulation box dimensions and give space for the atoms of the wall.
Thanks for your support.