Pulling protein through membrane without changing the position of membrane

From: Rabeta Yeasmin (rabetayeasmin_at_gmail.com)
Date: Thu May 11 2017 - 11:51:44 CDT


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

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