[gmx-users] Simulation problem with extended membrane system!

liu xin zgxjlx at gmail.com
Thu Sep 7 04:57:09 CEST 2006

Hi Chris
Thank you for your suggestions!

These days I also tried anisotropic and semiisotropic for my simulation, but
I still got the same result, so I wonder maybe there's something wrong with
my initial structure, but it will take time to check it out.

I'm trying to use the method you suggested, I searched the list, find there
is some scripts offered by other users, but I'm new to Linux and gromacs,
I've got no idea which one to use and how to use it. So would you please
send me a sample?

Thank you very much for your help

Xin Liu

On 9/5/06, chris.neale at utoronto.ca <chris.neale at utoronto.ca> wrote:
> It is unclear why your second method works for you. However, given that it
> does,
> just use genbox -cs spc216.gro -cp 183_system_that_worked.gro -box 9.2 9.2
> 8.3
> and then use your own script to remove any spc waters that were put inside
> the
> membrane and modify the nubers in your topology file accordingly.
> I imagine that your first attempt didn't work since an entire dppc
> molecule is
> removed upon a single collision and this will lead to "holes" in your
> membrane
> that will quickly fill with water. Of course this should also have
> happened in
> your second attempt... I am not sure what was different there.
> You need semiisotropic pressure coupling and you need to stop every once
> and a
> while and remove any water molecules that are inside the membrane. Note
> that
> isotropic Pcoupling in a membrane system (as you have been doing) has the
> potential to provide a surface tension (or the opposite) that you have not
> been
> intentionally including and so you can expect your membrane to behave
> differently.
> Chris.
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