I want to perform a MD simulation to investigate protein interaction with surfaces. The question I have is that If wanna to keep the distance between surface and protein as constant, I have to fix the center of mass of protein.
Can CHARMM do that? which command I should use?
or, to be simple, I can initially fix the atom which is very close to the center of mass of protein by using "CONS FIX " command during the simulation. I knew CHARMM can do it using the latter method. But, I don't know whether this method is reasonable ?