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

From: Rabeta Yeasmin (
Date: Mon May 15 2017 - 13:23:22 CDT

Thanks so much for the suggestion. It worked well.

Rabeta Yeasmin

On Thu, May 11, 2017 at 12:05 PM, Amy Rice <> wrote:

> 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 <>
> wrote:
>> 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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