[gmx-users] query about protein-ligand complex

[Mark Abraham]

sangeeta wrote:
> I could not mail you as our net was down, 
> you asked me "Is your system
>  properly minimized? "
> My question is how can I understand whether my system is properly minimised?

Look at the structure before you minimize it, and look at the structure 
after you minimize it. See what has changed and use some chemical 
judgement. If you're uncertain of yourself, experiment with some smaller 
systems before using a system as large as yours.

Mark