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

[Dallas Warren]

http://manual.gromacs.org/documentation/current/user-guide/run-time-errors.html#system-has-non-zero-total-charge

You will need to go through your topologies and work out why there is a
non-zero charge like that.

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 Thu, 1 Aug 2019 at 14:05, 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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