[gmx-users] non-zero total charge for water

[JMandumpal]

Dear Gromacs users,

I built .tpr file prior to energy minimisation of box of tip5p water molecule. I received the output like this:

calling /lib/cpp...
processing topology...
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 2 bonded neighbours for SOL 258
NOTE:
  System has non-zero total charge: -2.580000e-01
 
processing coordinates...
double-checking input for internal consistency...
Cleaning up constraints and constant bonded interactions with virtual sites
renumbering atomtypes...
converting bonded parameters...
#     SETTLE:   258
#  VSITE3OUT:   516
Setting particle type to V for virtual sites
initialising group options...
processing index file...
Analysing residue names:
Opening library file /opt/gromacs/3.3.2-dp/share/gromacs/top/aminoacids.dat
There are:   258      OTHER residues
There are:     0    PROTEIN residues
There are:     0        DNA residues
Analysing Other...
Making dummy/rest group for T-Coupling containing 1290 elements
Making dummy/rest group for Acceleration containing 1290 elements
Making dummy/rest group for Freeze containing 1290 elements
Making dummy/rest group for Energy Mon. containing 1290 elements
Making dummy/rest group for VCM containing 1290 elements
Number of degrees of freedom in T-Coupling group rest is 1545.00
Making dummy/rest group for User1 containing 1290 elements
Making dummy/rest group for User2 containing 1290 elements
Making dummy/rest group for XTC containing 1290 elements
Making dummy/rest group for Or. Res. Fit containing 1290 elements
Making dummy/rest group for QMMM containing 1290 elements
T-Coupling       has 1 element(s): rest
Energy Mon.      has 1 element(s): rest
Acceleration     has 1 element(s): rest
Freeze           has 1 element(s): rest
User1            has 1 element(s): rest
User2            has 1 element(s): rest
VCM              has 1 element(s): rest
XTC              has 1 element(s): rest
Or. Res. Fit     has 1 element(s): rest
QMMM             has 1 element(s): rest
Checking consistency between energy and charge groups...
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 175x175x175, spacing 0.115 0.115 0.115
writing run input file...
 
--------------------------------------------------

It says, System has non-zero total charge: -2.580000e-01.

What could be the problem. I tried to solve it, but I can't. what resulted the error?
I paste my top and itp files below.

sincerly,
Jestin


---------------------------------------------
topol.top

#include "ffoplsaa.itp"
#include "tip5P.itp"
                                                                                                                                                                                                     
[ system ]
Pure water
                                                                                                                                                                                                     
[ molecules ]
SOL 258
                                                                                                                                                                                                     

 
tip5P.itp file
----------------------------------------------------------------------- 
[ moleculetype ]
; molname   nrexcl
SOL         2
                                                                                                                                                                                                     
[ atoms ]
; id    at type res nr  residu name   at name    cg nr   charge
#ifdef _FF_OPLS
   1     opls_118    1    SOL      OW         1       0
   2     opls_119    1    SOL      HW1        1       0.24
   3     opls_119    1    SOL      HW2        1       0.241
   4     opls_120    1    SOL      LP1        1      -0.241
   5     opls_120    1    SOL      LP2        1      -0.241
                                                                                                                                                                                                     
[ settles ]
; i     funct   doh     dhh
1       1       0.09572 0.15139
                                                                                                                                                                                                     
[ dummies3 ]
; The position of the dummy is computed as follows:
;
; The distance from OW to OL is 0.07 nm, the geometry is tetrahedral
; (109.47 deg)
; Therefore, a =3D b =3D 0.07 * cos (109.47/2) / | xOH1 + xOH2 |
;            c =3D 0.07 * sin (109.47/2) / | xOH1 X xOH2 |
;           =20
;
; Using | xOH1 X xOH2 | =3D | xOH1 | | xOH2 | sin (H1-O-H2)
;       | xOH1 + xOH2 | =3D 2 | xOH1 | cos (H1-O-H2)
; Dummy pos x4 =3D x1 + a*x21 + b*x31 + c*(x21 X x31)
                                                                                                                                                                                                     
; Dummy from                    funct   a       b               c
4       1       2       3       4       -0.344908  -0.344908  -6.4437903493
5       1       2       3       4       -0.344908  -0.344908   6.4437903493
                                                                                                                                                                                                     
[ exclusions ]
1       2       3       4       5
2       1       3       4       5
3       1       2       4       5
4       1       2       3       5
5       1       2       3       4
#endif
~
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