I have the following problem:
I generate successfully in Polymer Modeler an initial configuration of PE (degree of polymerization 100, 26 chains) in a box of 50Ä.
Once in LAMMPS I want to have the PE on top of a region where I create a lattice of atoms with create_atoms.
The problem is that if I change the simulation box size in the data file I have the following initial result with long bonds between atoms (view down).
This leads to errors like "bond/angle/dihedral extent half of periodic box length".
How could I solve this?
I have found the "solution" of exporting from Polymod the wrapped input file in PDB format and generate the LAMMPS data file by means of VMD and Topotools.