LAMMPS, Large-scale Atomic/Molecular Massively Parallel Simulator, is a classical molecular dynamics (MD) code created for simulating molecular and atomic systems such as proteins in solution, liquid-crystals, polymers, zeolites, or simple Lenard-Jonesium. LAMMPS was originally developed as part of a 5-way DOE-sponsored CRADA collaboration between 3 industrial partners (Cray Research, Bristol-Myers Squibb, and Dupont) and 2 DoE laboratories (Sandia and Livermore). The current version of LAMMPS includes following features:

• parallelism via a spatial-decomposition algorithm
• short-range pairwise Lennard-Jones and Coulombic interactions
• long-range Coulombic interactions via Ewald or PPPM (particle-mesh Ewald)
• harmonic molecular potentials (bond, angle, torsion, improper)
• class II (cross-term) molecular potentials
• NVE, NVT, NPT dynamics
• constraints on atoms or groups of atoms, including SHAKE
• rRESPA long-timescale integrator
• energy minimizer (Hessian-free truncated Newton method)

submit_lammps [Job_name]
lammps_tool file1 [file2 ...]

Job_name.in file (command scripts) and Job_name.dat file (data file) will be needed to run jobs. The results are installed in Job_name.log file.