reg diffusion of water molecules

From: Vidhya Sankar (
Date: Sat Aug 12 2017 - 23:51:25 CDT

Thank you Namd users and chitrak gupta for your valuable suggestion about setting of periodic boundary condition for My system

For your reminder .
My system contain Assembly of cyclic peptide placed 2 Armstrong Distance above the Z axis of Lipid Membrane

 Lipid Membrane .
But when i run protein constrained equilibration , My water molecules on the head of lipid diffused upwards along assembly.Could you please suggest How can i solve the problem ? Is it possible by editing keep_water_out.tcl script . if it can which part of the tcl script should i edit ?
 I Request your valuable suggestion

With Regards

S.Vidhya sankar

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