Hard wall on Z direction for ions

From: Fateme Ghadirian (fateme.ghadirian_at_yahoo.com)
Date: Mon May 14 2018 - 09:06:31 CDT

Dear NAMD users,  

I have a POPEbilayer which is solvated in water and some ions just on the upper side ofmy membrane. During the run, due to the periodic boundarycondition, some of them go from the upper boundary and come from lower boundary,so I have some unwanted ions in the inner side of my box.

As a solution for this problem, I’ve used tclBCto apply a hard wall in Z direction, and added it to my conf file, thenperformed the simulation, but it did not work! So I still have unwanted ions inlower side of the box. The conf and tclBC files are incorporated to this email.

(TclBC code is written in a general case whichthere are ions in both sides of the membrane and also prevents PBC for ions inZ direction, clearly this is not the reason of the failure.)

Is there anyone who knows why this is notworking?

 Best Regards, 
 Fateme


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