GROMACS has this function, however that software is designed for proteins. TurboMole has this function, but is not a biomolecular MD suite.

Lennart, that wasn't a very helpful remark. I am aware that the purpose of MD is to change the conformation... there are also times when you want to change only a portion of the conformation and keep another portion rigid.

rmv: I will try SHAPEs. I checked out that link you provided and am still figuring out the syntax for my needs. I have already tried CONS HARM BESTFIT and didn't get the desired effect.