[gmx-users] tpr generation aborted

Mahmood Naderan nt_mahmood at yahoo.com
Sat Feb 24 15:59:33 CET 2018

Following the Lusozume tutorial, I face an error at the step of generating ions.tpr which says too many warnings.

$ gmx grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr
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 -723452053
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 topol.top, line 18409]:
  System has non-zero total charge: 8.000000
  Total charge should normally be an integer. See
  for discussion on how close it should be to an integer.

WARNING 1 [file topol.top, line 18409]:
  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.

J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof
Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net
J. Chem. Theory Comput. 10 (2014) pp. 381-393
-------- -------- --- Thank You --- -------- --------

Removing all charge groups because cutoff-scheme=Verlet
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
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 60x60x60, spacing 0.117 0.117 0.117
Estimate for the relative computational load of the PME mesh part: 0.22
This run will generate roughly 3 Mb of data

There were 2 notes

There was 1 warning

Program:     gmx grompp, version 2018
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2406)

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

Is it safe to use -maxwarn option?


More information about the gromacs.org_gmx-users mailing list