Repulsion of lipid bilayer during equilibration

From: Mahrukh Imtiaz (
Date: Fri Jul 22 2016 - 05:00:41 CDT

Hi,I am running MD simulations of p-glycoprotein embedded in lipid bilayer, following the namd tutorial of membrane proteins(Kcsa) but I got some problem during equlibration. Melting of lipid tails went fine but in the next step (equilibration with protein constrained), it seems strong repulsive forces are tearing lipid apart alongwith increase (around 10A) in box size. By the end of equilibration it looks like lipid has been vanished. I could not understand the reason.
However, I think there might be a problem with the "keep water out" tcl script. In the script, where water exceptions are defined, i did not specify any water index (kept empty bracket) as i wanted to make sure not a single water molecule enters the lipid channel. Kindly guide me if I am making some mistake here.


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