I was wondering when the prd command is being called, is there any way to exclude some particular atoms from velocity randomization?
More specifically, I’m (slowly) pulling an atom that’s harmonically bonded with a larger system. The velocity of atom is supposed to be constant, and the top layer of the larger system should be moving as a rigid body throughout the process. However, those two constraints seem to be messed up by prd’s velocity randomization.
Any tricks to get around this issue? Thank you all very much!