About keep_water_out.tcl

From: zeynab mohamad hoseyni (zmhoseyni_at_yahoo.com)
Date: Thu Feb 20 2014 - 05:21:23 CST

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Dear All, I used "keep_water_out.tcl" script within the preparation steps of my system composed of a trans-membrane protein crossed the  lipid bilayer solvated in the waters. The preparation step was then followed by the production run (NPT) when the mentioned tcl was turned off. Everything is OK till 6ns when I see some water molecules penetrate a small cavity located on the protein-lipid interface close to the intra-cellular part. Does any-body has any solution for that? Is it OK to use the mentioned script within  the production run and does it affect the results? All the Best, Zeynab

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