[gmx-users] System has non-zero total charge: 1.999878e+00

[Mark Abraham]

zakiya wrote:
> Hi Gromacs users,
> I have some problems about the total charge of system using Gromacs.
> I wanted to perform a protein denaturation simulation induced by urea. At first, I added urea molecules into the box including one CI2 protein. Then I performed the energy minimization step. However, there’s a note that “NOTE 1 [file ci2.top, line 3998]:  System has non-zero total charge: 1.999878e+00 “.
> My question is that why the total charge of system is not an integer. The whole charge of CI2 protein is 2.000e+00. 

Arithmetic on computers is subject to rounding errors after each
operation. There are a number of threads on this list that have
discussed this in the past. So long as the total charge is still close
to an integer, you don't have evidence of a serious problem. See also
http://oldwiki.gromacs.org/index.php/Errors#System_has_non-zero_total_charge

Mark

I got the ITP file of urea molecule from the “share” file in the Gromacs
library directory. The total charge is zero. So this phenomena puzzled me.
> The [atoms] field in the ITP file of urea molecule is as follows:
> [ atoms ]
> ;   nr    type   resnr  residu    atom    cgnr  charge   mass
> #ifdef Boek
>      1       C       1    UREA      C1       1       0.38      12.0110
>      2       O       1    UREA      O2       1       -0.38    15.9994
>      3      NT       1    UREA      N3       2       -0.83    14.0067
>      4       H       1    UREA      H4       2       0.415    1.0080
>      5       H       1    UREA      H5       2       0.415    1.0080
>      6      NT       1    UREA      N6       3       -0.83     14.0067
>      7       H       1    UREA      H7       3     0.415    1.0080
>      8       H       1    UREA      H8       3       0.415    1.0080
> #else
>      1       C       1    UREA      C1       1       0.683    12.0110
>      2       O       1    UREA      O2       1       -0.683   15.9994
>      3      NT       1    UREA      N3       2       -0.622   14.0067
>      4       H       1    UREA      H4       2       0.346   1.0080
>      5       H       1    UREA      H5       2       0.276   1.0080
>      6      NT       1    UREA      N6       3       -0.622   14.0067
>      7       H       1    UREA      H7       3     0.346   1.0080
>      8       H       1    UREA      H8       3       0.276   1.0080
> #endif
>  
> Any help/suggestions will be greatly appreciated!
>  
> Thank you!!
> Na  Zhang
>  
> 
> 
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