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

[Dallas Warren]

This shows why posting the entire output is important.  The note is
not the reason why grompp failed, the warning is what you need to take
note of and respond to/deal with.  If you are doing the step here to
add the counter-ions to neutralise charge, then do as the information
at the bottom is telling you to do, ignore the warning and proceed.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Mon, 24 Jun 2019 at 18:54, kalpana <kalpanadynasty at gmail.com> wrote:
>
> 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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