membrane simulation and mobility of lipids - blocking ion channel

From: Jorgen Simonsen (
Date: Wed Sep 28 2011 - 09:07:50 CDT

Hi all,

I am doing a MD simulation of an ion channel protein. So I do observe
a strange thing in one of my simulation - one of the lipid head groups
is more or less blocking the channel entrance the gramicidin I am
using. If I followed the tutorial with nanotubes in membranes I get a
lipid molecule inside in the nanotube - as I am not doing many
membrane simulation - I do not know of this is something often
observed and how is this treated. My simulations are around 80 ns and
the temperature is 330 K - any advise highly appreciated

Thanks in advance,

Best regards

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