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

Mark Abraham mark.j.abraham at gmail.com
Sun Jun 30 23:24:28 CEST 2019


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.


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

> 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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