# Error in gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr commands **URL:** \ **Category:** User discussions\ **Created:** [August 24, 2024, 11:32am UTC](https://gromacs.bioexcel.eu/t/error-in-gmx-grompp-f-ions-mdp-c-solv-gro-p-topol-top-o-ions-tpr-commands/9973 "2024-08-24T11:32:08Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![z.esfahani](https://avatars.discourse-cdn.com/v4/letter/z/77aa72/32.png) [@z.esfahani](https://gromacs.bioexcel.eu/u/z.esfahani)\ **Post date:** [August 24, 2024, 11:32am UTC](https://gromacs.bioexcel.eu/t/error-in-gmx-grompp-f-ions-mdp-c-solv-gro-p-topol-top-o-ions-tpr-commands/9973/1 "2024-08-24T11:32:08Z")
GROMACS version: 2022.3 GROMACS modification: Yes/No Here post your question Hello everyone I’m getting these warnings and note. please guide me.thanks! And my forcefield is OPLS. Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /home/zahra/Desktop/lysozyme Command line: gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr Ignoring obsolete mdp entry ‘ns\_type’ NOTE 1 [file ions.mdp]: With Verlet lists the optimal nstlist is \>= 10, with GPUs \>= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Setting the LD random seed to 267836927 Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 3 bonded neighbours molecule type ‘Protein\_chain\_A’ Excluding 2 bonded neighbours molecule type ‘SOL’ Excluding 2 bonded neighbours molecule type ‘SOL’ NOTE 2 [file topol.top, line 18410]: System has non-zero total charge: 8.000000 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 18410]: 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: 129 Protein residues There are: 12144 Water residues Analysing Protein… Number of degrees of freedom in T-Coupling group rest is 78741.00 The largest distance between excluded atoms is 0.443 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 64x64x64, spacing 0.115 0.115 0.115 Estimate for the relative computational load of the PME mesh part: 0.27 This run will generate roughly 3 Mb of data There were 2 notes There was 1 warning * * * Program: gmx grompp, version 2022.3 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2661) 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) ---
**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\ **Post date:** [August 24, 2024, 1:52pm UTC](https://gromacs.bioexcel.eu/t/error-in-gmx-grompp-f-ions-mdp-c-solv-gro-p-topol-top-o-ions-tpr-commands/9973/2 "2024-08-24T13:52:14Z")
Dear @z.esfahani As the warning reports, you have net charge (+8) in your system. You can’t (or shouldn’t) run MD sims with net charge leftover in your system. You have to neutralize the box by adding the appropriate amount of counter ions, for example with `gmx genion`. Take a look at [this tutorial](http://www.mdtutorials.com/gmx/lysozyme/index.html) as well, which might guide you in the set up of the systems.