[gmx-users] geometry optimization of metalloenzyme

Nadia Elghobashi-Meinhardt nelgho at gmail.com
Sun Mar 29 17:50:39 CEST 2020


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.


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