; ; forcefield by Lubos Vrbka for (contaminated) ice simulations ; Lubos Vrbka, 2006 ; lubos (@) vrbka (.) net ; ; water parameters - nada/van der eerden ; implementation by marcelo carignano (cari (@) purdue (.) edu) ; nacl parameters - j. chem. phys. 100, 3757 ; implementation by marcelo carignano (cari (@) purdue (.) edu) ; used with spc/e - consistency? ; alcohol parameters - AMBER parm99 parameters ; implementation by lubos vrbka (lubos (@) vrbka (.) net) ; ; changed gen-pairs to yes (consistently with amber FF) - should not affect ; NE6 water potential #define _FF_ICE [ defaults ] ; nbfunc comb-rule gen-pairs FudgeLJ FudgeQQ 1 2 yes 0.5 0.8333 ; ************************************************************************* [ atomtypes ] ;name type mass charge ptype c6 c12 ; original AMBER atom types: CT, H1, HC, OH, HO ; CT sp3 carbon (charge corresponding to CH3!) ; H1 hydrogen bound to C with el. withdrawing substituent ; HC hydrogen bound to C ; HO hydroxyl hydrogen ; OH hydroxyl oxygen ; name btype mass charge ptype sigma epsilon CT CT 12.010 0.1116 A 3.39967e-01 4.57730e-01 HC HC 1.0080 0.0372 A 2.64953e-01 6.56888e-02 H1 H1 1.0080 0.0372 A 2.47135e-01 6.56888e-02 ;HO HO 1.0080 0.4215 A 2.47135e-01 6.56888e-02 HO HO 1.0080 0.4215 A 0.00000e+00 0.00000e+00 OH OH 16.0000 -0.6497 A 3.06647e-01 8.80314e-01 ; NE6 water model EP EP 0.00000 -0.866 D 0.00000E+00 0.00000E+00 OW OW 15.99940 0.000 A 3.11500E-01 0.714850050 HW HW 1.00800 0.477 A 6.73000E-02 0.115419008 LP LP 0.00000 -0.477 D 0.00000E+00 0.00000E+00 ; sections [ ????types ] contain generic alcohol contaminant params [ bondtypes ] ; i j func b0 kb HO OH 1 0.09600 462750.4 CT OH 1 0.14100 267776.0 CT CT 1 0.15260 259408.0 CT H1 1 0.10900 284512.0 CT HC 1 0.10900 284512.0 [ angletypes ] ; i j k func th0 cth CT OH HO 1 108.500 460.240 CT CT OH 1 109.500 418.400 CT CT CT 1 109.500 334.720 CT CT HC 1 109.500 418.400 CT CT H1 1 109.500 418.400 HC CT HC 1 109.500 292.880 H1 CT H1 1 109.500 292.880 H1 CT OH 1 109.500 418.400 [ dihedraltypes ] ; i j k l func coefficients ;CT CT OH HO 3 1.71544 0.96232 0.00000 -2.67776 0.00000 0.00000 ;CT CT CT OH ;CT CT CT CT 3 3.68192 3.09616 -2.09200 -3.01248 0.00000 0.00000 ;CT CT CT HC 3 0.66944 2.00832 0.00000 -2.67776 0.00000 0.00000 ;CT CT CT H1 3 0.66944 2.00832 0.00000 -2.67776 0.00000 0.00000 ;H1 CT OH HO ;HC CT CT H1 ;HC CT CT HC 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.0000 ;HC CT CT OH 3 1.04600 -1.04600 0.00000 0.00000 0.00000 0.00000 X CT CT X 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 X CT OH X 3 0.69733 2.09200 0.00000 -2.78933 0.00000 0.00000 ; ************************************************************************* [ moleculetype ] ; molname nrexcl 5OL 3 [ atoms ] ; id at type res nr resname at name cg nr charge 1 HO 1 5OL HO 1 0.420 2 OH 1 5OL OH 1 -0.648 3 CT 1 5OL C01 1 0.154 4 H1 1 5OL H11 1 0.037 5 H1 1 5OL H12 1 0.037 6 CT 1 5OL C02 1 -0.074 7 HC 1 5OL H21 1 0.037 8 HC 1 5OL H22 1 0.037 9 CT 1 5OL C03 1 -0.074 10 HC 1 5OL H31 1 0.037 11 HC 1 5OL H32 1 0.037 12 CT 1 5OL C04 1 -0.074 13 HC 1 5OL H41 1 0.037 14 HC 1 5OL H42 1 0.037 15 CT 1 5OL C05 1 -0.111 16 HC 1 5OL H51 1 0.037 17 HC 1 5OL H52 1 0.037 18 HC 1 5OL H53 1 0.037 [ bonds ] ; values defined after the defaults section ; i j funct b0 kb 1 2 1 2 3 1 3 4 1 3 5 1 3 6 1 6 7 1 6 8 1 6 9 1 9 10 1 9 11 1 9 12 1 12 13 1 12 14 1 12 15 1 15 16 1 15 17 1 15 18 1 [ angles ] ; values defined after the defaults section ; i j k funct th0 cth 1 2 3 1 2 3 4 1 2 3 5 1 2 3 6 1 3 6 7 1 3 6 8 1 3 6 9 1 6 9 10 1 6 9 11 1 6 9 12 1 9 12 13 1 9 12 14 1 9 12 15 1 12 15 16 1 12 15 17 1 12 15 18 1 4 3 5 1 4 3 6 1 7 6 8 1 7 6 9 1 10 9 11 1 10 9 12 1 13 12 14 1 13 12 15 1 16 15 17 1 16 15 18 1 [ dihedrals ] ; values defined after the defaults section ; i j k l func coefficients 1 2 3 4 3 1 2 3 5 3 1 2 3 6 3 2 3 6 7 3 2 3 6 8 3 2 3 6 9 3 3 6 9 10 3 3 6 9 11 3 3 6 9 12 3 6 9 12 13 3 6 9 12 14 3 6 9 12 15 3 9 12 15 16 3 9 12 15 17 3 9 12 15 18 3 4 3 6 7 3 4 3 6 8 3 4 3 6 9 3 5 3 6 7 3 5 3 6 8 3 5 3 6 9 3 7 6 9 10 3 7 6 9 11 3 7 6 9 12 3 8 6 9 10 3 8 6 9 11 3 8 6 9 12 3 10 9 12 13 3 10 9 12 14 3 10 9 12 15 3 11 9 12 13 3 11 9 12 14 3 11 9 12 15 3 13 12 15 16 3 13 12 15 17 3 13 12 15 18 3 14 12 15 16 3 14 12 15 17 3 14 12 15 18 3 ;[ pairs ] ; i j funct c6 c12 ;1 4 1 ;1 5 1 ;1 6 1 ;1 7 1 ;2 5 1 ;2 6 1 ;2 7 1 ;3 6 1 ;3 7 1 ;4 7 1 ; ************************************************************************* [ moleculetype ] ; molname nrexcl NE6 1 [ atoms ] ; We use a strange order of atoms to make things go faster in GROMACS (?) ; id at type res nr resname at name cg nr charge 1 HW 1 NE6 HW1 1 0.477 2 HW 1 NE6 HW2 1 0.477 3 LP 1 NE6 LP1 1 -0.044 4 LP 1 NE6 LP2 1 -0.044 5 EP 1 NE6 EP 1 -0.866 6 OW 1 NE6 OW 1 0.000 [ constraints ] ; i j funct distance 1 6 1 0.0980 ; HW1 - OW 2 6 1 0.0980 ; HW1 - OW 1 2 1 0.15857 ; HW1 - HW2 [ dummies3 ] ; For the EP: ; Dummy from funct a b 5 6 1 2 1 0.199642537 0.199642537 ; For the LPs: ; Dummy from funct a b c 3 6 1 2 4 -0.437172 -0.437172 8.022961206 4 6 1 2 4 -0.437172 -0.437172 -8.022961206 [ exclusions ] 1 2 3 4 5 6 2 1 3 4 5 6 3 1 2 4 5 6 4 1 2 3 5 6 5 1 2 3 4 6 6 1 2 3 4 5