GROMACS
http://www.gromacs.org/
Assisted Model building with Energy Refinement (AMBER)
https://ambermd.org/
LAMMPS
https://lammps.sandia.gov/
NAMD
http://www.ks.uiuc.edu/Research/namd/
Chemistry at HARvard Macromolecular Mechanics (CHARMM)
https://www.charmm.org//charmm/documentation/