[gmx-users] fixing protein during energy minimization

[Mark Abraham]

Vaibhav Saraf wrote:
> Hi all,
> 
> Can we fix the protein along with its water of crystallization, while
> doing energy minimization with some additional water molecules? if
> yes, how?

Yes, they're called "position restraints". If you're serious about doing 
MD in GROMACS, please read about the first five chapters of the manual 
first. It's quite good, and reading it will help you avoid making silly 
mistakes, and avoid you not being aware of clearly-stated functionality.

Mark