right, Jim...no cheating

Jim: "....maybe you can simulate the movement using the temp setting instead of having the "computer" push it."

And thanks! (see comments last post)

I'm working on it. I am using some thermostats to create a temperature differential. From the Nanorex wiki:

"Attaches a Langevin Thermostat to a single selected atom, thereby associating the thermostat to the entire molecule of which the selected atom is a member. The user specifies the temperature (in Kelvin). The Langevin Thermostat is used to set and hold the temperature of a molecule during a simulation run..."

I have to split up the tube into two separate ones. The sim is currently running, I'll post more details later.