1; 2; Topology file for SW 3; 4; Paul van Maaren and David van der Spoel 5; Molecular Dynamics Simulations of Water with Novel Shell Model Potentials 6; J. Phys. Chem. B. 105 (2618-2626), 2001 7; 8; Force constants for the shell are given by: 9; 10; k = qs^2/(4 pi eps0 alpha) 11; However, in the current version of the itp file and software (3.2+) 12; force constants are computed in mdrun, and the input is the 13; polarizability in nm^3. 14; 15; Some data: mu (water) = 1.8546 D ( 0.0386116 e nm) 16; 1/(4 pi eps0 alpha) = 94513.94 17; 18; Alpha-X = 1.415 kx = 608069 19; Alpha-Y = 1.528 ky = 563101 20; Alpha-Z = 1.468 kz = 586116 21; 22; Alpha = 1.470 k = 585318 23; 24; Bonding parameters from (but without cubic term): 25; D. M. Ferguson: 26; Parametrization and Evaluation of a Flexible Water Model 27; J. Comp. Chem. 16(4), 501-511 (1995) 28; 29; Possible defines that you can put in your topol.top: 30; -DANISOTROPIC Select anisotropic polarizibility (isotropic is default). 31; -DRIGID Rigid model (flexible is default) 32; -DPOSRES Position restrain oxygen atoms 33; 34 35[ defaults ] 36LJ Geometric 37 38[ atomtypes ] 39;name mass charge ptype c6 c12 40 WO 15.99940 0.0 A 0.0 0.0 41 WH 1.00800 0.0 A 0.0 0.0 42 WS 0.0 0.0 S 0.0 0.0 43 WD 0.0 0.0 D 0.0 0.0 44 45[ nonbond_params ] 46#ifdef RIGID 47#ifdef ANISOTROPIC 48WH WH 1 4.0e-5 4.0e-8 49WS WO 1 1.0e-6 1.0e-12 50WS WH 1 4.0e-5 2.766e-08 51WO WO 1 2.0e-3 1.174e-06 52#else 53WH WH 1 4.0e-5 4.0e-8 54WS WO 1 1.0e-6 1.0e-12 55WS WH 1 4.0e-5 2.769e-08 56WO WO 1 2.0e-3 1.176e-06 57#endif 58#else 59#ifdef ANISOTROPIC 60WH WH 1 4.0e-5 4.0e-8 61WS WO 1 1.0e-6 1.0e-12 62WS WH 1 4.0e-5 2.910e-08 63WO WO 1 2.0e-3 1.189e-06 64#else 65WH WH 1 4.0e-5 4.0e-8 66WS WO 1 1.0e-6 1.0e-12 67WS WH 1 4.0e-5 2.937e-08 68WO WO 1 2.0e-3 1.187e-06 69#endif 70#endif 71 72;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 73;; This is a the 'classical YAW' model, in which we do have the dummy. 74;; The shell is attached to the dummy, in this case the gas-phase 75;; quadrupole is correct. Water_pol routine can be used for this 76;; model. This has four interaction sites. 77;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 78[ moleculetype ] 79; molname nrexcl 80SW 2 81 82[ atoms ] 83; id at type res nr residu name at name cg nr charge 841 WO 1 SM2 OW1 1 1.24588 852 WH 1 SM2 HW2 1 0.62134 863 WH 1 SM2 HW3 1 0.62134 874 WD 1 SM2 DW 1 0.0 885 WS 1 SM2 SW 1 -2.48856 89 90#ifdef ANISOTROPIC 91[ water_polarization ] 92; See notes above. Alphas in nm^3 (See ref. above) 93; O H H D S funct al_x al_y al_z rOH rHH rOD 94 1 2 3 4 5 1 0.001415 0.001528 0.001468 0.09572 0.15139 0.0137408 95 96#else 97 98[ polarization ] 99; See notes above. alpha (nm^3) 1004 5 1 0.00147 101#endif 102 103#ifdef RIGID 104[ settles ] 105; i funct dOH dHH 1061 1 0.09572 0.15139 107 108#else 109 110[ bonds ] 1111 2 1 0.09572 458148. 1121 3 1 0.09572 458148. 113 114[ angles ] 115; i j k 1162 1 3 1 104.52 417.6 117#endif 118 119[ dummies3 ] 120; The position of the dummies is computed as follows: 121; 122; O 123; 124; D 125; 126; H H 127; 128; 2 * b = distance (OD) / [ cos (angle(DOH)) * distance (OH) ] 129; 0.0137408 nm / [ cos (104.52 / 2 deg) * 0.09572 nm ] 130; 0.01557 nm 131; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-X1) 132; 133; Dummy from funct a b 1344 1 2 3 1 0.117265878 0.117265878 135 136[ exclusions ] 137; iatom excluded from interaction with i 1381 2 3 4 5 1392 1 3 4 5 1403 1 2 4 5 1414 1 2 3 5 1425 1 2 3 4 143 144#ifdef POSRES 145; Restrain the oxygen... 146[ position_restraints ] 147; iatom type fx fy fz 1481 1 100 100 100 149#endif 150 151