Generating ion.tpr file


I am getting the following error from Lysozyme in water tutorial. I successfully completed this tutorial a few months ago but this week it seems the file gets broken at the ions.tpr output step. Please see message and file generated.

Command line:
gmx grompp -f ions.mdp -c 1AKI_solv.gro -p -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 -471713371
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’

NOTE 2 [file, line 18409]:
System has non-zero total charge: 8.000000
Total charge should normally be an integer. See
Floating point arithmetic — GROMACS webpage documentation
for discussion on how close it should be to an integer.

Analysing residue names:
There are: 129 Protein residues
There are: 10644 Water residues
Analysing Protein…
Number of degrees of freedom in T-Coupling group rest is 69741.00

NOTE 3 [file ions.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.

This run will generate roughly 3 Mb of data

There were 3 notes


What makes you think the file is broken, does the next step involving gmx genion fail? The .tpr is a binary file so it’s not supposed to be human-readable, and your gmx grompp output seems just fine.

Hi yes thank you so much. I successfully completed the tutorial and got the right graphs at the end. Thank you I did not know the files were meant to be binary.