Fatal Error: Too many warnings (1) Use -maxwarn option in gromacs 2023.2

User discussions
1

Respected Sir/Ma’am,
I am getting an error as shown below.
:-) GROMACS - gmx grompp, 2023.2 (-:

Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /home/drr-18/Complex_02_EMinimized
Command line:
gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -r nvt.gro -p topol.top -n index.ndx -o npt.tpr

Ignoring obsolete mdp entry ‘title’
Ignoring obsolete mdp entry ‘ns_type’

WARNING 1 [file npt.mdp]:
The Berendsen barostat does not generate any strictly correct ensemble,
and should not be used for new production simulations (in our opinion).
We recommend using the C-rescale barostat instead.

Setting the LD random seed to -346112009

Generated 167799 of the 167910 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1

Generated 117432 of the 167910 1-4 parameter combinations

Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’

turning H bonds into constraints…

Excluding 3 bonded neighbours molecule type ‘LIG’

turning H bonds into constraints…

Excluding 2 bonded neighbours molecule type ‘SOL’

turning H bonds into constraints…

Excluding 3 bonded neighbours molecule type ‘SOD’

turning H bonds into constraints…

The center of mass of the position restraint coord’s is 4.533 4.519 4.529

The center of mass of the position restraint coord’s is 4.533 4.519 4.529
Number of degrees of freedom in T-Coupling group Protein_LIG is 15247.69
Number of degrees of freedom in T-Coupling group Water_SOD is 134421.31

The largest distance between excluded atoms is 0.447 nm between atom 2465 and 5645

Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K

Calculated rlist for 1x1 atom pair-list as 1.294 nm, buffer size 0.094 nm

Set rlist, assuming 4x4 atom pair-list, to 1.221 nm, buffer size 0.021 nm

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

NOTE 1 [file npt.mdp]:
Removing center of mass motion in the presence of position restraints
might cause artifacts. When you are using position restraints to
equilibrate a macro-molecule, the artifacts are usually negligible.

Reading Coordinates, Velocities and Box size from old trajectory

Will read whole trajectory
Last frame -1 time 100.000

Using frame at t = 100 ps

Starting time for run is 0 ps
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 60x60x60, spacing 0.151 0.151 0.151

Estimate for the relative computational load of the PME mesh part: 0.14

This run will generate roughly 41 Mb of data

There was 1 NOTE

There was 1 WARNING

Program: gmx grompp, version 2023.2
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

GROMACS version:
GROMACS modification: Yes/No
Here post your question : I don’t know about this error, i tried the solution to use -maxwarn flag. But still i am not able to get rid off this error during NPT Equilibration Thank you in advance.

2

Additional Information in the file grompp.cpp (src/gromacs/gmxpreprocess/grompp.cpp (line 2691))
done_warning(wi, FARGS);
write_tpx_state(ftp2fn(efTPR, NFILE, fnm), ir, &state, sys);

/* Output IMD group, if bIMD is TRUE */
gmx::write_IMDgroup_to_file(ir->bIMD, ir, &state, sys, NFILE, fnm);

sfree(opts->define);
sfree(opts->wall_atomtype[0]);
sfree(opts->wall_atomtype[1]);
sfree(opts->include);
sfree(opts->couple_moltype);

for (auto& mol : mi)
{
    // Some of the contents of molinfo have been stolen, so
    // fullCleanUp can't be called.
    mol.partialCleanUp();
}
done_inputrec_strings();
output_env_done(oenv);

return 0;
3

The simplest answer is to follow the suggestion provided in the error message and not use the Berendsen algorithm.