[gmx-users] non-zero total charge for water
JMandumpal
jesbman at rediffmail.com
Fri Dec 14 01:35:27 CET 2007
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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