[gmx-users] Constraints Error; In Using Tetrahedral Zinc Dummy Model

[Mark Abraham]

Hi,

The usual way to do this is with harmonic bonds (or equivalent distance
restraints) from metal to ligand. Those are different from constraints.
GROMACS is not built for general rigid-body motion, which is what a
fully-constrained tetrahedron would require.

Mark


On Sun, 30 Jun 2019 at 20:32, Mahdi Bagherpoor <mehdi.bpour at gmail.com>
wrote:

> Dear Gromacs users,
>
> I am trying to simulate a zinc-finger protein in explicit water, *with
> CHARMM36 FF*. Unfortunately, I did not find any *tetrahedral zinc force*
> field
> in Gromacs and therefore I converted the tetrahedral dummy zinc model used
> in CHARMM27 FF to the format of Gromacs. The minimization of the system
> goes perfect but unfortunately when I start *NVT simulation*, I get this
> error:
> ------------
>
> WARNING 1 [file topol.top, line 57]:
>   The bond in molecule-type Dummy_chain_X between atoms 2 DZ1 and 3 DZ2 has
>   an estimated oscillational period of 6.1e-03 ps, which is less than 5
>   times the time step of 2.0e-03 ps.
>   Maybe you forgot to change the constraints mdp option.
> ...
> Too many warnings (1).
> If you are sure all warnings are harmless, use the -maxwarn option.
>
> -----------
> Here, DZ1 and DZ2 are dummy atoms related to tetrahedral zinc model. *in
> mdp file*, I have used *h-bonds* *Lincs* constraint. When I use the
> *all-bond* in the mdp file again I get another error that is:
> -----------
>
> WARNING 1 [file topol.top, line 57]:
>   There are atoms at both ends of an angle, connected by constraints and
>   with masses that differ by more than a factor of 13. This means that
>   there are likely dynamic modes that are only very weakly coupled. To
>   ensure good equipartitioning, you need to either not use constraints on
>   all bonds (but, if possible, only on bonds involving hydrogens) or use
>   integrator = sd or decrease one or more tolerances:
>   verlet-buffer-tolerance <= 0.0001, LINCS iterations >= 2, LINCS order >=
>   4 or SHAKE tolerance <= 1e-05
> ....
> Number of degrees of freedom in T-Coupling group Protein_DNA_ZNT is 6936.89
> Number of degrees of freedom in T-Coupling group Water_and_ions is
> 179547.11
> ....
>
> ------------
> Does this error mean that I need to constraint zinc bonds beside h-bonds?
> If so, how should I do it? or something wrong in my topology is? *I will
> appreciate* if you let me know any idea to fix this problem.
>
> Cheers,
> Mahdi
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