Have you tried gromacs?

https://www.gromacs.org/About_Gromacs

If you run the simulation, then you can calculate rmsd, rg, etc, by the trajectory files.

Also, see this page of Justin Lemkul:

http://www.mdtutorials.com/gmx/

I think Francisco J. Enguita will be able to help here.

Best,

Maryam

Reliable and free rarely go together.

See CHARMM-GUI:

CHARMM-GUI is a web-based platform to build inputs of well-established biomolecular simulations packages. It not performs MD, but could help you with some steps:

https://www.charmm-gui.org/

I deeply appreciate your prompt suggestions so far. Many thanks. Additional suggestions are, however, also welcome.

http://chemyang.ccnu.edu.cn/ccb/server/LARMD/