[gmx-users] EM broke protein-lipid system

[Mark Abraham]

On 21/06/2011 2:46 AM, Du Jiangfeng (BIOCH) wrote:
> Dear Gromacs Users,
> It comes to me with million problems per day during I am using gromacs. :(

Computational chemistry is rarely easy. The tasks are complex and 
demanding, even when the software is mature and the documentation well 
written... That said, you're tackling a difficult multi-phase system...

> Maybe you are the right persons i should ask about coarse grained protein-lipid simulation. Right now I have a system with a bilayer (DOPCs) and a protein (Histone). After EM simulation, it worked quite well.... Then, this system was filled with water and was performed by EM again. Then it was scattered severely. Though I tried lipid constraint and many other methods, the problem is still here....
> Any suggestions?

I can only suggest that you find and follow suitable tutorial material, 
simplifying your system as much as you can, adding complexity in stages.

Mark