GROMACS version:2018

Hi dear users,

I want to perform MD simulation on a protein containing 3 Zn ions by amber99sb force field.by -his and CYM and applying distance restraint, zn ions fixed in their position with out any movement but after energy minimization I got the bellow warnings,now I do not know how to change nvtmdp parameters number to solve the problem.

''WARNING 1 [file topol.top, line 86896]:

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_ZN is 18332.72

Number of degrees of freedom in T-Coupling group NA_CL_Water is 177762.28

Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K

Calculated rlist for 1x1 atom pair-list as 0.935 nm, buffer size 0.035 nm

Set rlist, assuming 4x4 atom pair-list, to 0.900 nm, buffer size 0.000 nm

Note that mdrun will redetermine rlist based on the actual pair-list setup

Calculating fourier grid dimensions for X Y Z

Using a fourier grid of 64x72x60, spacing 0.151 0.155 0.158

Estimate for the relative computational load of the PME mesh part: 0.19

This run will generate roughly 8 Mb of data’’