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Comparing Simulations of Methionine Aminopeptidase in LAMMPS and GROMACS

Jacob Perez
Department of Earth and Planetary Sciences, University of Tennessee

This page shows visualization of methionine aminopeptidase from E. coli. The structures were generated using CHARMM-GUI1,2 through Im Lab at Lehigh University. The MD simulations were performed on a custom build of LAMMPS made courtesy of Dr. Dayton Kizzire at the University of Tennessee, Knoxville.

Two simulations of a methionine aminopeptidase were ran in different molecular dynamics software: LAMMPS and GROMACS. Each simulation followed similar procedural steps for energy minimization and system equilibration. The data production process was a lot faster for GROMACS and allowed for an order of magnitude longer simulation time for only 1.5 times longer the walltime. The trajectories were very similar in both LAMMPS and GROMACS. However, GROMACS preserved the structural information (i.e., secondary structures like helices and sheets) of the peptidase. The LAMMPS simulation was limited to describing atomistic detail in its trajectory (top structure) while GROMACS can demonstrate detail on specific residues and secondary structures (bottom structure). It is important to note that the rotation shown in the GROMACS movie is not the actual motion of the enzyme but instead the view rotating around the enzyme. Preservation of the secondary structures along with computational efficiency in simulating long times demonstrates how well-tuned GROMACS is to simulating biological systems compared to LAMMPS.

Interactive Structures

Color Legend:

  • carbon = grey
  • hydrogen = white
  • nitrogen = blue
  • oxygen = red
  • sulfur = yellow


1. Lee, J, et al. 2016. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations using the CHARMM36 Additive Force Field. J. Chem. Theory Comput. 12. 405-413, doi: 10.1021/acs.jctc.5b00935

2. Jo, S, Kim, T, Iyer, VG, and Im, W. 2008. CHARMM-GUI: A Web0based Graphical User Interface for CHARMM. J. Comput. Chem. 29. 1859 - 1865, doi: 10.1002/jcc.20945

posted: May 2022.
updated: May 2022.