[gmx-users] fixing protein during energy minimization
mahnam at ibb.ut.ac.ir
Tue Feb 6 08:31:56 CET 2007
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.
Institute of Biochemistry and Biophysics (IBB)
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