[gmx-users] geometry optimization of metalloenzyme

[Nadia Elghobashi-Meinhardt]

Hello everyone,

I am trying to minimize the potential energy of a
metalloenzyme containing Ni and Fe atoms.
What is the best way to constrain (fix?) the position of the active site
atoms
during the geometry optimization?
I have tried introducing bonds with relatively high force constants and
alternatively, tried introducing a [constraints] section,
but the atoms are still not staying put.
Or should one use extra position restraints?

Any tips are welcome!
Thank you.