From: Rabeta Yeasmin (rabetayeasmin_at_gmail.com)
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?
This archive was generated by hypermail 2.1.6 : Wed Dec 11 2019 - 23:19:38 CST