[gmx-users] big protein dynamics

[Adriana Pietropaolo]

On Wed, 30 Nov 2005, Tsjerk Wassenaar wrote:

> Hi Adriana,
> 
> Did you energy minimize your system before this?
> 
> A pretty robust regime to follow is:
> 
> 1. energy minimize in vacuum
> 2. energy minimize after solvation
> 3. perform position restrained MD
> 4. run a short simulation with temperature coupling to equilibrate
> 5. turn on pressure coupling and let the system equilibrate
> 6. harvest
> 
> Cheers,
> 
> Tsjerk

Yes, it's a structure just minimize...
maybe the position of some water molecules are within the protein 
backbone...
I try to minimize the box with both protein and water...
thanks!
Adriana