<P>
Dear Gromacs users,<BR>
<BR>
I built .tpr file prior to energy minimisation of box of tip5p water molecule. I received the output like this:<BR>
<BR>
calling /lib/cpp...<BR>
processing topology...<BR>
Generated 332520 of the 332520 non-bonded parameter combinations<BR>
Generating 1-4 interactions: fudge = 0.5<BR>
Generated 332520 of the 332520 1-4 parameter combinations<BR>
Excluding 2 bonded neighbours for SOL 258<BR>
NOTE:<BR>
System has non-zero total charge: -2.580000e-01<BR>
<BR>
processing coordinates...<BR>
double-checking input for internal consistency...<BR>
Cleaning up constraints and constant bonded interactions with virtual sites<BR>
renumbering atomtypes...<BR>
converting bonded parameters...<BR>
# SETTLE: 258<BR>
# VSITE3OUT: 516<BR>
Setting particle type to V for virtual sites<BR>
initialising group options...<BR>
processing index file...<BR>
Analysing residue names:<BR>
Opening library file /opt/gromacs/3.3.2-dp/share/gromacs/top/aminoacids.dat<BR>
There are: 258 OTHER residues<BR>
There are: 0 PROTEIN residues<BR>
There are: 0 DNA residues<BR>
Analysing Other...<BR>
Making dummy/rest group for T-Coupling containing 1290 elements<BR>
Making dummy/rest group for Acceleration containing 1290 elements<BR>
Making dummy/rest group for Freeze containing 1290 elements<BR>
Making dummy/rest group for Energy Mon. containing 1290 elements<BR>
Making dummy/rest group for VCM containing 1290 elements<BR>
Number of degrees of freedom in T-Coupling group rest is 1545.00<BR>
Making dummy/rest group for User1 containing 1290 elements<BR>
Making dummy/rest group for User2 containing 1290 elements<BR>
Making dummy/rest group for XTC containing 1290 elements<BR>
Making dummy/rest group for Or. Res. Fit containing 1290 elements<BR>
Making dummy/rest group for QMMM containing 1290 elements<BR>
T-Coupling has 1 element(s): rest<BR>
Energy Mon. has 1 element(s): rest<BR>
Acceleration has 1 element(s): rest<BR>
Freeze has 1 element(s): rest<BR>
User1 has 1 element(s): rest<BR>
User2 has 1 element(s): rest<BR>
VCM has 1 element(s): rest<BR>
XTC has 1 element(s): rest<BR>
Or. Res. Fit has 1 element(s): rest<BR>
QMMM has 1 element(s): rest<BR>
Checking consistency between energy and charge groups...<BR>
Calculating fourier grid dimensions for X Y Z<BR>
Using a fourier grid of 175x175x175, spacing 0.115 0.115 0.115<BR>
writing run input file...<BR>
<BR>
--------------------------------------------------<BR>
<BR>
It says, System has non-zero total charge: -2.580000e-01.<BR>
<BR>
What could be the problem. I tried to solve it, but I can't. what resulted the error?<BR>
I paste my top and itp files below.<BR>
<BR>
sincerly,<BR>
Jestin<BR>
<BR>
<BR>
---------------------------------------------<BR>
topol.top<BR>
<BR>
#include "ffoplsaa.itp"<BR>
#include "tip5P.itp"<BR>
<BR>
[ system ]<BR>
Pure water<BR>
<BR>
[ molecules ]<BR>
SOL 258<BR>
<BR>
<BR>
<BR>
tip5P.itp file<BR>
----------------------------------------------------------------------- <BR>
[ moleculetype ]<BR>
; molname nrexcl<BR>
SOL 2<BR>
<BR>
[ atoms ]<BR>
; id at type res nr residu name at name cg nr charge<BR>
#ifdef _FF_OPLS<BR>
1 opls_118 1 SOL OW 1 0<BR>
2 opls_119 1 SOL HW1 1 0.24<BR>
3 opls_119 1 SOL HW2 1 0.241<BR>
4 opls_120 1 SOL LP1 1 -0.241<BR>
5 opls_120 1 SOL LP2 1 -0.241<BR>
<BR>
[ settles ]<BR>
; i funct doh dhh<BR>
1 1 0.09572 0.15139<BR>
<BR>
[ dummies3 ]<BR>
; The position of the dummy is computed as follows:<BR>
;<BR>
; The distance from OW to OL is 0.07 nm, the geometry is tetrahedral<BR>
; (109.47 deg)<BR>
; Therefore, a =3D b =3D 0.07 * cos (109.47/2) / | xOH1 + xOH2 |<BR>
; c =3D 0.07 * sin (109.47/2) / | xOH1 X xOH2 |<BR>
; =20<BR>
;<BR>
; Using | xOH1 X xOH2 | =3D | xOH1 | | xOH2 | sin (H1-O-H2)<BR>
; | xOH1 + xOH2 | =3D 2 | xOH1 | cos (H1-O-H2)<BR>
; Dummy pos x4 =3D x1 + a*x21 + b*x31 + c*(x21 X x31)<BR>
<BR>
; Dummy from funct a b c<BR>
4 1 2 3 4 -0.344908 -0.344908 -6.4437903493<BR>
5 1 2 3 4 -0.344908 -0.344908 6.4437903493<BR>
<BR>
[ exclusions ]<BR>
1 2 3 4 5<BR>
2 1 3 4 5<BR>
3 1 2 4 5<BR>
4 1 2 3 5<BR>
5 1 2 3 4<BR>
#endif<BR>
~<BR>
</P>
<br><br>
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