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

Mahdi Bagherpoor mehdi.bpour at gmail.com
Sun Jun 30 02:00:15 CEST 2019

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? *I will appreciate* if you let me know any idea
to fix this problem.


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