| -verbose 7 | Verbose output. |
| -size 10,10,10 | Simulation box size (angstrom). |
| -bonds intra | Generate all or intramolecular bonds only. |
| -wrap | Wrap around (periodic boundaries). |
| -timestep 0.01 | Integration time step (default 0.001). |
| -velocitylimit 0.01 | Limit on the velocity (default 0.1 per time step). |
| -friction 0.2 | Friction constant (default 1 = no friction). |
| -Kbond 150 | Bond strength (default 1). |
| -Kangle 4 | Angle strength (default 1). |
| -Kvdw 0.1 | Van der Waals strength (default 0). |
| -Kelectrostatic 0.4 | Electrostatic strength (default 0). |
| -cutoff 7.8 | Distance cutoff for non-bonded forces (default 5 A). |
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