Membrane/peptide system. Water moving from one layer to the other ...

From: Villalain Boullon, Jose (
Date: Wed Oct 23 2013 - 05:46:00 CDT

Dear All,


First of all, thank you very much for your help. It is always encouraging that you can rely on people pertaining to this forum to resolve the problems which arise trying to work with NAMD (at least for me as a newbie).


Sorry, but I have a new problem which I have not seen previously. I am using the configuration files from the membrane-protein tutorial, but some simulations, not all, show that there is a displacement of the water layer/membrane structure. I will try to explain. The water thickness of one layer increases steadily as the other one decreases steadily, like water is moving from one layer to the other. Seen from the other way, it is like the whole membrane is moving, downwards/upwards.


Any hint to resolve this strange behaviour ?

Best regards,



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