[gmx-users] Fwd: geometry optimization of metalloenzyme

[Nadia Elghobashi-Meinhardt]

Thank you, Justin.
I am still struggling with constraints.
I am trying to use "freezegrps" and "freezedim"
to run an NVT equilibration.
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"
What do these messages indicate? Problem in memory allocation?

On Thu, Apr 2, 2020 at 9:26 PM Justin Lemkul <jalemkul at 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
>
> jalemkul at 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-request at gromacs.org.
>