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
8 ; Force constants for the shell are given by:
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.
15 ; Some data: mu (water) = 1.8546 D ( 0.0386116 e nm)
16 ; 1/(4 pi eps0 alpha) = 94513.94
18 ; Alpha-X = 1.415 kx = 608069
19 ; Alpha-Y = 1.528 ky = 563101
20 ; Alpha-Z = 1.468 kz = 586116
22 ; Alpha = 1.470 k = 585318
24 ; Bonding parameters from (but without cubic term):
26 ; Parametrization and Evaluation of a Flexible Water Model
27 ; J. Comp. Chem. 16(4), 501-511 (1995)
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
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
49 WS WO 1 1.0e-6 1.0e-12
50 WS WH 1 4.0e-5 2.766e-08
51 WO WO 1 2.0e-3 1.174e-06
54 WS WO 1 1.0e-6 1.0e-12
55 WS WH 1 4.0e-5 2.769e-08
56 WO WO 1 2.0e-3 1.176e-06
61 WS WO 1 1.0e-6 1.0e-12
62 WS WH 1 4.0e-5 2.910e-08
63 WO WO 1 2.0e-3 1.189e-06
66 WS WO 1 1.0e-6 1.0e-12
67 WS WH 1 4.0e-5 2.937e-08
68 WO WO 1 2.0e-3 1.187e-06
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 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
83 ; id at type res nr residu name at name cg nr charge
84 1 WO 1 SM2 OW1 1 1.24588
85 2 WH 1 SM2 HW2 1 0.62134
86 3 WH 1 SM2 HW3 1 0.62134
88 5 WS 1 SM2 SW 1 -2.48856
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
99 ; See notes above. alpha (nm^3)
111 1 2 1 0.09572 458148.
112 1 3 1 0.09572 458148.
120 ; The position of the dummies is computed as follows:
128 ; 2 * b = distance (OD) / [ cos (angle(DOH)) * distance (OH) ]
129 ; 0.0137408 nm / [ cos (104.52 / 2 deg) * 0.09572 nm ]
131 ; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-X1)
133 ; Dummy from funct a b
134 4 1 2 3 1 0.117265878 0.117265878
137 ; iatom excluded from interaction with i
145 ; Restrain the oxygen...
146 [ position_restraints ]
147 ; iatom type fx fy fz