I am using BIOVIA Materials Studio (Forcite MD) to analyze a vapor/liquid system, where the liquid layer is in the middle of the cell. I want to calculate a density profile along the z-axis using the Concentration profiles in Forcite --> analysis. However, the liquid layer is moved along z-axis during MD runs, so the concentration cannot be calculated correctly. My question is how to remove such an unwanted translational motion of the cell? so that the z-directed concentration profile could be calculated correctly? If there is any script for such a problem, I would like to have a copy. Your help is highly appreciated. Thank you very much.
Attached is a snapshot of the trajectory at t= 0 and at t=5 ns.
