Thank you, Justin. I am still struggling with constraints. I am trying to use "*freezegrps*" and "*freezedim*" to run an NVT equilibration of a structure (successfully geometry-optimized using freezegrps).
However, when I try to build the binary using my optimized structure, I get either "Segmentation fault" or the following error: "free(): invalid next size (fast) Aborted" These messages seem to indicate a memory allocation problem, but I cannot isolate the problem. I am not sure of the correct combination of constraint (lincs) keywords in the nvt input, especially how to combine these with the freezegrps/freezedim commands. Do anybody have any tips or helpful examples? On Thu, Apr 2, 2020 at 9:26 PM Justin Lemkul <jalem...@vt.edu> wrote: > > > 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. > -- 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.