[gmx-users] fixing protein during energy minimization

[Mahnam]

In God We Trust
Hello Dear Vaibhav Saraf 
 > My system consists of the protein, water of crystallization and
> additional water molecules. And before doing the position restraint
> MD, I wish to perform energy minimization once with the protein and
> its water of crystallisation fixed and only the additional water
> molecules free. Later would do it un-restrained.
> So need guidance on whether I can fix the protein (along with its
> water of crystallisation) during energy minimization

you can make an index file and make a fix group consists  of number of 
protein and water of crystallization and then in mdp file define freezegrps 
and freezedim ( Y Y Y ) and with MD integrator.

Yours truly 
Karim Mahnam
Institute of  Biochemistry  and  Biophysics (IBB)
Tehran University 
P.O.box 13145-1384
Tehran 
Iran 
http://www.ibb.ut.ac.ir/
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