Output Files

Every generate run writes into <System out>/<name>/:

my_polymer/polyethylene/
├── moltemplate/           # Intermediate files (.lt inputs, moltemplate output)
├── system.data            # LAMMPS data file (topology & coordinates)
├── system.in.init         # Units, atom/bond/angle styles
├── system.in.settings     # Force field parameters
└── system.in.charges      # Atomic charges

The files

File	Contents
system.data	The LAMMPS data file: box dimensions, masses, atoms, bonds, angles, dihedrals — full topology and coordinates
system.in.init	Simulation header: units, atom_style, bond_style, angle_style, dihedral_style, pair_style, boundary conditions
system.in.settings	Force field parameters: pair_coeff, bond_coeff, angle_coeff, dihedral_coeff entries for every type in the system
system.in.charges	Atomic partial charges (Gasteiger charges for GAFF/GAFF2 — replace with AM1-BCC/RESP for production)
moltemplate/	Everything moltemplate produced: the monomer .lt templates, the assembled system.lt, and moltemplate's raw output

Running with LAMMPS

Include the pieces from your own input script:

lmp -in your_run.in

# your_run.in
include system.in.init      # styles and units
read_data system.data       # topology and coordinates
include system.in.settings  # force field parameters

# ... your minimization / equilibration / production commands

Equilibrate in stages

Initial boxes are built at low density for overlap-free placement. Minimize → NVT heating → NPT compression → NPT production, with a 0.5–1.0 fs timestep for atomistic systems.

Bead-spring output

BeadSpringPolymer writes a single self-contained LAMMPS data file (including all coefficients in reduced units) instead of the system.in.* split — see the Bead-Spring guide.