[gmx-users] freez group

[Mark Abraham]

Morteza Khabiri wrote:
> Dear Mark,
> 
> thanks for your suggestion...the position restrain is very good idea which
> I did it before..but I just restrain protein and after some time ligand
> start to come out..I think my problem is that I don't know how to restrain
> ligand?
> It will be nice of you if tell me how to restrain ligand?

Depending what you want to do, either use position restraints on the 
ligand while equilibrating, or distance restraints on the ligand while 
equilibrating or simulating, or (if the ligand should stay bound of its 
own accord) get a physical model that works.

Mark