[gmx-users] Energy Minimization

[Mark Abraham]

On 10/01/2012 9:54 PM, Steven Neumann wrote:
> Dear Gmx Users,
> I am setting up my simulations of carbon tube with protein. I solvated 
> my system, added ions and I would like to run EM of my system. My 
> carbons of the tube in MD will be restrained. In this case should I 
> run EM of my protein in water (and with ions) separately and the copy 
> coordinates and then process with NVT and NPT or run EM with 
> restrained nanotubes of my system directly?

The former is less likely to have problems.

Mark