Error in gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr commands

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1

GROMACS version: 2022.3
GROMACS modification: Yes/No
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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
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

2

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 as well, which might guide you in the set up of the systems.