# Problems trying to add ions

**URL:** <https://gromacs.bioexcel.eu/t/problems-trying-to-add-ions/6754>\
**Category:** User discussions\
**Created:** [July 4, 2023, 1:10pm UTC](https://gromacs.bioexcel.eu/t/problems-trying-to-add-ions/6754 "2023-07-04T13:10:18Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Miriam](https://avatars.discourse-cdn.com/v4/letter/m/c89c15/32.png) [@Miriam](https://gromacs.bioexcel.eu/u/Miriam)\
**Post date:** [July 4, 2023, 1:10pm UTC](https://gromacs.bioexcel.eu/t/problems-trying-to-add-ions/6754/1 "2023-07-04T13:10:18Z")

</div>

GROMACS version: 2023.1  
GROMACS modification:No

Hi  
im trying to run this line:  
gmx\_mpi grompp -f ions.mdp -c beta\_solvated.gro -p topol.top -o beta\_pp\_ionize.tpr

And the following error comes up. I don’t understand why, of course there a charge, that’s why I want to add ions.  
I’m using amber99sb-ildn FF.  
Thanks!

Ignoring obsolete mdp entry ‘ns\_type’  
Setting the LD random seed to 1434415062

Generated 2145 of the 2145 non-bonded parameter combinations  
Generating 1-4 interactions: fudge = 0.5

Generated 2145 of the 2145 1-4 parameter combinations

Excluding 3 bonded neighbours molecule type ‘Protein’

Excluding 2 bonded neighbours molecule type ‘SOL’

NOTE 1 [file topol.top, line 1089]:  
System has non-zero total charge: -2.000000  
Total charge should normally be an integer. See  
[Floating point arithmetic — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Floating_Point_Arithmetic)  
for discussion on how close it should be to an integer.

WARNING 1 [file topol.top, line 1089]:  
You are using Ewald electrostatics in a system with net charge. This can  
lead to severe artifacts, such as ions moving into regions with low  
dielectric, due to the uniform background charge. We suggest to  
neutralize your system with counter ions, possibly in combination with a  
physiological salt concentration.

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++  
J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof  
Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net  
Charge  
J. Chem. Theory Comput. 10 (2014) pp. 381-393  
-------- -------- — Thank You — -------- --------

Analysing residue names:  
There are: 9 Protein residues  
There are: 2578 Water residues  
Analysing Protein…  
Number of degrees of freedom in T-Coupling group rest is 23523.00  
The integrator does not provide a ensemble temperature, there is no system ensemble temperature

The largest distance between excluded atoms is 0.405 nm between atom 23 and 31  
Calculating fourier grid dimensions for X Y Z  
Using a fourier grid of 42x42x42, spacing 0.116 0.116 0.116

Estimate for the relative computational load of the PME mesh part: 0.25

This run will generate roughly 2 Mb of data

There was 1 NOTE

There was 1 WARNING

* * *

Program: gmx grompp, version 2023.1  
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2691)

Fatal error:  
Too many warnings (1).  
If you are sure all warnings are harmless, use the -maxwarn option.

## For more information and tips for troubleshooting, please check the GROMACS website at [Common Errors — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Errors)

Abort(1) on node 0 (rank 0 in comm 0): application called MPI\_Abort(MPI\_COMM\_WORLD, 1) - process 0

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<div class="post-metadata">

**Author:** ![Carsten](https://avatars.discourse-cdn.com/v4/letter/c/f14d63/32.png) [@Carsten](https://gromacs.bioexcel.eu/u/Carsten)\
**Post date:** [July 5, 2023, 9:04am UTC](https://gromacs.bioexcel.eu/t/problems-trying-to-add-ions/6754/2 "2023-07-05T09:04:37Z")

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Dear Miriam,

`grompp` does not know that the `.tpr` file you are producing will just serve as an input file for `gmx genion` in a second step. Therefore, you can safely add the` -maxwarn 1` option to `grompp` and proceed from there.

Best regards,  
Carsten