Lipid bilayer deformed during coarse grain simulation

From: Rabeta Yeasmin (
Date: Fri Feb 09 2018 - 10:58:19 CST

Dear NAMD users,

I am running coarse grain simulation of the lipid bilayer-protein system. I
have converted the lipid-protein all-atom system to coarse grain system
using residue-based coarse-graining method and then add water and ions in
it. I have used some extra bonds between two monomers of the protein so
that they do not fall apart during simulation. But after running the
equilibration steps, I have checked the trajectories and found the lipid
bilayer deformed during the simulation. It changed to some arbitrary shape
from the rectangular shape.

I am wondering why it can happen and how can I solve this problem?


Rabeta Yeasmin

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