# [gmx-users] Charge system simulation problem

Justin Lemkul jalemkul at vt.edu
Mon Nov 26 15:58:23 CET 2018

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On 11/26/18 12:01 AM, Karpurmanjari Kakati wrote:
> Dear All,
>
> My System contains, while doing NVT of the same, I got the following Note
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> *NOTE 1 [file sa.top, line 80]:  System has non-zero total charge:
> 12.936997  Total charge should normally be an integer. See
> http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> <http://www.gromacs.org/Documentation/Floating_Point_Arithmetic>  for
> discussion on how close it should be to an integer.*
>
>
> This is possibly because of  the partial charges in the molecules in the
> ITP fie.

Something isn't parametrized correctly because you need to have an
integer charge. Your total charge is not physical.

-Justin

> My doubt is can't I have a system with non zero and a decimal charge value.
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> Also I got the following warning:
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> *WARNING 1 [file sa.top, line 80]:  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.*
>
> Can Someone help me with this?
>
> Also this :
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> *Velocities were taken from a Maxwell distribution at 300 KRemoving all
> charge groups because cutoff-scheme=VerletAnalysing residue names:There
> are:     1      Other residuesThere are: 100000      Water residues*
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> Removing all charge group because the cut off scheme is verlet.
>
> If That happens then will it show the behavior I want to see. Or shall I
> put any other scheme on that ?
>

--
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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