On 4/2/20 3:23 PM, Nadia Elghobashi-Meinhardt wrote:
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.
Bonds or constraints will maintain distances between atoms (relative position) but not absolute position.
Or should one use extra position restraints?
If the absolute position matters, yes. I would think the approach of adding restraints or constraints between atoms would be more meaningful given that preserving coordination geometry is often the defect in MM treatment of transition metals.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
