Re: membrane simulation and mobility of lipids - blocking ion channel

From: HAMID - (
Date: Thu Sep 29 2011 - 04:33:48 CDT

Hi Jorgen,

I also encounter to such problem at early steps of all system relaxed
MD. Did the channel block in early steps (after minimization and
equilibration) or the problem persists throughout the all system
relaxed MD?


On 9/28/11, Jorgen Simonsen <> wrote:
> 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

H. Hadi
PhD student of Biophysics,
UT, Iran

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