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
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?
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:20:17 CST