[gmx-users] System has non-zero total charge

Dallas Warren dallas.warren at monash.edu
Wed May 22 00:19:23 CEST 2019


"If the charge is already close to an integer, then the difference is
caused by rounding errors and not a major problem."

If want to pursue further, there are discussions and comments by
developers on this emailing list addressing the issue.

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 Wed, 22 May 2019 at 03:56, Shadi Fuladi <sfulad2 at uic.edu> wrote:
> Hi,
> Running grompp I get the NOTE "System has non-zero total charge: 0.000180".
> I have been running this electrolyte system which includes multiple
> molecules before without a problem. There are ions in the system as well as
> polar molecules (via atomic partial charges). The total charge of each
> molecule is an integer. I am trying to change the number and ratio of
> molecules now and I get this NOTE. And it only happens when number of ions
> is more than number of polar molecules.
> As before I am preparing the initial structure using insert-molecules or
> PACKMOL. And topol.top file looks proper.
> How can I address this NOTE? If I don't want to ignore it - since it wasn't
> happening before for same molecules only different ratio.
> I appreciate your help,
> Shadi
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