[gmx-users] Charge system simulation problem

[Karpurmanjari Kakati]

Hi Justin,

Because I have self generated the itp file, and that's the only place where
charge in terms of partial charge is added. Is the problem lying there?
Also can't  we denote the partial charges in decimal because  in real some
atoms will have net charges that can be decimal values due to presence or
absence of electronegative atoms adjacent to it?


And are all the other notes and warnings generated are all because of that?


karpurmanjari

On Mon, Nov 26, 2018 at 10:31 AM Karpurmanjari Kakati <
ch18resch01002 at iith.ac.in> 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.
> My doubt is can't I have a system with non zero and a decimal charge value.
>
>
> 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*
>
>
> 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 ?
>
> Please help
>
>