[gmx-users] How to deal with "non-zero total charge" problem in gromacs?

[Dallas Warren]

Go through the topologies, residue by residue, find where it deviates. Each
residue should sum to an integer charge.

Also look at how you generated the topology, actually steps involved, where
the coordinate files came from etc. Somewhere a choice has been made,
process performed that introduced this problem.

On Thu, 1 Aug. 2019, 3:18 pm sunyeping, <sunyeping at aliyun.com> wrote:

>
>
> ------------------------------------------------------------------
> From:Bratin Kumar Das <177cy500.bratin at nitk.edu.in>
> Sent At:2019 Aug. 1 (Thu.) 12:31
> To:gromacs <gmx-users at gromacs.org>; 孙业平 <sunyeping at aliyun.com>
> Subject:Re: [gmx-users] How to deal with "non-zero total charge" problem
> in gromacs?
>
> Hi,
>     Yes you can use the (-maxwarn) flag to overcome the error. But better
> to optimize the starting structure to reduce the excess charge of your
> system.
>
> Thank you for the replay. But I have no idea of how to optimize the
> starting structure to reduce the excess charge. Could you give me some
> hints or examples or something?
>
> Best regards
>
>
>
> On Thu, Aug 1, 2019 at 9:35 AM sunyeping <sunyeping at aliyun.com> wrote:
> Dear all,
>
>  I am trying to do MD simulation with protein-DNA complex with gromacs.
> When using gmx grompp to generate the tpr file for energy minimization, I
> enconters a fatal error:
>
>  Fatal error:
>  Too many warnings (1).
>  If you are sure all warnings are harmless, use the -maxwarn option.
>
>  There are two notes and one warning arose with grompp, and they are:
>
>  NOTE 1 [file em.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.
>  NOTE 2 [file topol.top, line 55]:
>    System has non-zero total charge: -0.189598
>    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 55]:
>    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.
>
>  It seems that the -0.189598 non-zero charge causes the fatal error. Is it
> possible to correct it? and how? or could I use the -maxwarn option as
> mentioned in the error message?
>
>  Best regards
>  --
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