[gmx-users] Fwd: (-13.000000 Total charge should normally be an integer), Facing problem while running gromacs

[kalpana]

Thanks a lot for your prompt response. I thought the fetal error is due to
as its saying non-interger charge but i am not getting the output file to
add ions to neutralize charge. The complete report is this:

  gmx grompp -f ions.mdp -c model1_solv.gro -p topol.top -o ions.tpr

Setting the LD random seed to -1944004748
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 1 [file topol.top, line 60959]:
  System has non-zero total charge: -13.000000
  Total charge should normally be an integer. See
  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 60959]:
  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 --- -------- --------

Cleaning up constraints and constant bonded interactions with virtual sites
Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are:   424    Protein residues
There are: 16324      Water residues
Analysing Protein...
Number of degrees of freedom in T-Coupling group rest is 117267.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 80x80x80, spacing 0.116 0.116 0.116
Estimate for the relative computational load of the PME mesh part: 0.26
This run will generate roughly 6 Mb of data

There was 1 note

There was 1 warning

-------------------------------------------------------
Program:     gmx grompp, version 2019.3
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2315)

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 http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

On Mon, Jun 24, 2019 at 11:22 AM Bratin Kumar Das <
177cy500.bratin at nitk.edu.in> wrote:

> It is telling that system have -13 charge...Which need to be neutralise by
> gmx genion command
>
> On Mon 24 Jun, 2019, 11:09 AM Alex, <nedomacho at gmail.com> wrote:
>
> > It is not an error message, but a note. If grompp quits with an error,
> > please read it carefully.
> >
> > Alex
> >
> > On 6/23/2019 11:27 PM, kalpana wrote:
> > > Kindly help to understand this error message becz with previous
> > > installation with same setting files, there was no error. The error
> > message
> > > is as follows:
> > >
> > >                gmx grompp -f  ions.mdp -c model1_solv.gro -p topol.top
> -o
> > > ions.tpr
> > >
> > >                Setting the LD random seed to 31221519
> > >                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 1 [file topol.top, line 60959]:
> > >                System has non-zero total charge: -13.000000
> > >                Total charge should normally be an integer. See
> > >
> > http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> > >                for discussion on how close it should be to an integer.
> > >
> > > Best regards
> > > Kalpana
> > --
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