the method to move freely in one direction like a rigid body

From: Xiaokang Liu (
Date: Mon May 25 2015 - 05:46:40 CDT

Hello NAMD users,

I want to implement a procedure in my simulation but I don't know the detailed process.

My simulation system consists two identical artificial membranes with a pore in the center made up of a carbon nanotube and two parallel graphene sheets in x and y directions. Two NaCl solutions of different concentrations are separated by the two membranes. The concentration between the membranes is higher so water will flow from the bilateral chambers to the middle one through the nanotube because of osmotic pressure. If the membranes are both fixed, hydrostatic pressure in the middle chamber will increase. But I want to keep the pressure of all chambers remain unchanged, so I think one possible method is to fix one membrane and keep the other one move freely in the z direction according to the force imposed on it.

So the problem is how to remain one membrane removable in z direction just like a rigid one according to the bilateral forces. Is this realizable in NAMD?

Any advice would be appreciated.
Thank you.

Xiaokang Liu

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