[gmx-users] Bug with system total charge?

[DimitryASuplatov]

Hello,

I am running a simulation of a protein in 10M urea (Smith topology) and spce water.

I run energy minimization in vacuum, then use genbox to add mixed solvent, then run grompp and receive the following message:
System has non-zero total charge: -8.999696e+00

Then I use genion to add 80 NA+ and 71 CL- (I use opls) in exchange on SOL molecules. Resulting top file looks like this

===========================================
#define HEAVY_H

; Include forcefield parameters
#include "ffoplsaa.itp"

; Include chain topologies
#include "1klc.5toA.300.urea.spce_A.itp"
#include "1klc.5toA.300.urea.spce_B.itp"

; Include water topology
#include "urea.smith.itp"
#include "spce.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_A           1
Protein_B           1
UREA            5130
SOL         15796
NA+         80
CL-	    71
=======================================================

Everything seems fine but when I run grompp again to start energy minimization in solvent I receive a devastating comment:

  System has non-zero total charge: 3.043525e-04
!!!

No complaints about incompatibility between top and gro. The order of groups in top and in gro are synchronized (PROTEIN, UREA, SOL, NA+, CL-).
I tried to add only 1 NA+ and this changed the result to: System has non-zero total charge: -7.999696e+00
2NA+:   System has non-zero total charge: -6.999696e+00
1NA+ and 1CL- :   System has non-zero total charge: -8.999696e+00
71NA+ and 71CL-: System has non-zero total charge: -8.999696e+00
73NA+ and 71CL-:   System has non-zero total charge: -6.999696e+00
75NA+ and 71CL-:   System has non-zero total charge: -4.999696e+00
77NA+ and 71CL-:   System has non-zero total charge: -2.999696e+00
78NA+ and 71CL-: System has non-zero total charge: -1.999696e+00
79NA+ and 71CL-:   System has non-zero total charge: -9.996956e-01 !!!!!!!!!!!!!!!
and finally 
80NA+ and 71CL-:  System has non-zero total charge: 3.043525e-04 !!!!!!!! 

Number of ions included by genion is always appropriate. Number of UREA atoms always stays the same. I tried gromacs 4.0.4 and 4.0.2 - same result!

Never had that problem before. Must be some issue with urea topology but I can not figure it out myself. Any suggestions?
Thanks.
SDA