From: Jeffrey Potoff (jpotoffx_at_gmail.com)
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".?
Jeff
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 jpotoff_at_wayne.edu 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 http://potoff1.eng.wayne.edu ======================================================================
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:18 CST