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: -2.58e-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: 0PROTEIN residues
There are: 0DNA 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
User1has 1 element(s): rest
User2has 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: -2.58e-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 ]
; idat type res nr residu name at namecg nr charge
#ifdef _FF_OPLS
1 opls_1181SOL OW 1 0
2 opls_1191SOL HW11 0.24
3 opls_1191SOL HW21 0.241
4 opls_1201SOL LP11 -0.241
5 opls_1201SOL LP21 -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)
