Re: Lipid bilayer tears apart during simulation

From: Jeffrey Potoff (
Date: Fri Jun 14 2013 - 15:46:10 CDT

Need more information to give a good answer. Could be a lot of things.
How did you build the bilayer? Do you have ions in the system? What
force field are you using? How did you determine the length of the x, y
and z-axis for the simulation cell?

My initial suspicion is that you don't have the correct x-y dimensions
(box is too big in the x-y plane). What happens if you run NPT
simulations with "useConstantRatio = yes".?


On 6/14/2013 4:14 PM, Peterson J wrote:
> Hi all,
> I am currently simulating a membrane protein homology model embedded
> in lipid bilayer and performed simulated annealing and lipid melting
> steps successfully. But when the system is subjected under
> equilibration simulation (NVT) with constraints only on protein Ca
> atoms, I see the lipid bilayer tearing apart.
> What are the possible solution to solve this?
> Thanks,
> Peterson

Jeffrey J. Potoff               
Associate Professor and Director of Early Engineering Programs
Department of Chemical Engineering and Materials Science
Wayne State University			  5050 Anthony Wayne Dr
Detroit, MI 48202

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:18 CST