[gmx-users] Fwd: 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 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 <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
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