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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