The best replacement for namd is gromacs.

The best alternatives to namd are rated as following:
★★★★★  gromacs
★★★  charmm
★★  lammps
★  desmond

Your alternative for namd is not listed? Suggest!
Speaking about namd, one probably shouldn't forget about vmd.

Other search terms related to namd and their ratings are:
★★★★★ vmd
You have in mind a companion for namd and it is not yet here? Propose!



Google Trends

Scale is based on the average worldwide traffic of namd in all years. Click on graph for more.
namd
gromacs
charmm