[gmx-users] Charge system simulation problem

Karpurmanjari Kakati ch18resch01002 at iith.ac.in
Mon Nov 26 06:01:54 CET 2018

Dear All,

My System contains, while doing NVT of the same, I got the following Note

*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>  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:

*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 :

*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

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