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LAMMPSLarge-Scale Atomic/Molecular Massively Parallel Simulator
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We used LAMMPS [11] package for all our simulations with default thermostat (Nose-Hoover chain) and barostat (implemented by Sinhoda et.
Supported applications include: OpenFOAM, NUMECA, Acusolve, LS-Dyna, Gaussian, Gamess, NAMD, Gromacs, LAMMPS, BLAST, FASTA, HMMER, ClustalW and OntoStudio.
To realistically represent both structure and dynamics over the great length and time scales of the system, we will use two well-established, parallel, coarse-grained molecular dynamic simulators: LAMMPS (large-scale atomic/molecular massively parallel simulator) and MHR (molecular high roller).