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. 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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