Re: Pulling protein through membrane without changing the position of membrane

From: Amy Rice (
Date: Thu May 11 2017 - 12:05:37 CDT

Hi Rabeta,
I faced a similar problem a few months back, and found that restraining
just the z-component of the lipid headgroups worked fairly well. This
allows the lipids to move in xy to settle around the protein but should
keep them from translocating with it.

Hope this helps,
- Amy

On Thu, May 11, 2017 at 11:51 AM, Rabeta Yeasmin <>

> Hi,
> I am trying to pull protein across the membrane bilayer to translate it in
> z direction without changing the position of membrane. I have set up the
> simulation in charmm-gui with a greater water thickness outside the
> membrane than the usual one so that even though protein move out of the
> membrane, it can be in water. I was using constant force pulling. But I am
> facing three types of problems-
> 1. If I fix all the atoms of the membrane or some specific atoms like N,
> HN1, HN2, HN3 position; the protein does not translate, it's side atoms
> just move.
> 2. If I fix just N, or N and HN1 atom of membrabe, the system become
> unstable immediately due to constraint error.
> 3. If I do not fix anything, the protein translate but it takes some part
> of membrane with it while translating which I do not want.
> Can anyone please help me about how to fix it?
> Rabeta Yeasmin

Amy Rice
Ph.D. Student
Physics Department
Illinois Institute of Technology

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