[gmx-users] Re: Polarizable water model
Dr. Vitaly V. Chaban
vvchaban at gmail.com
Thu Jul 21 05:38:30 CEST 2011
>>> Is any polarizable water models are available in ITP format? Or may be I
>>> should prepare .itp from some articles? In recent mail archive I've found
>>> some mentions about SWFLEX-AI model. Also I've found van der Spoel's
>>> article. May be somebody have ready .itp files of some models?
>>>
>
>>There should be a file with polarizable water topology in the standard
>>topology folder of the gromacs installation.
>
> I thought the same but I couldn't find it! Could you point me? I found
> only tip3,4,5p variants, spc variants and f3c. No of them has fluctuating
> charge or dipole so no electronic polarization is simulated, isn't it?
>
=======================================
; Paul van Maaren and David van der Spoel
; Molecular Dynamics Simulations of Water with Novel Shell Model Potentials
; J. Phys. Chem. B. 105 (2618-2626), 2001
;
; Force constants for the shell are given by:
;
; k = qs^2/(4 pi eps0 alpha)
; However, in the current version of the itp file and software (3.2+)
; force constants are computed in mdrun, and the input is the
; polarizability in nm^3.
;
; Some data: mu (water) = 1.8546 D ( 0.0386116 e nm)
; 1/(4 pi eps0 alpha) = 94513.94
;
; Alpha-X = 1.415 kx = 608069
; Alpha-Y = 1.528 ky = 563101
; Alpha-Z = 1.468 kz = 586116
;
; Alpha = 1.470 k = 585318
;
; Bonding parameters from (but without cubic term):
; D. M. Ferguson:
; Parametrization and Evaluation of a Flexible Water Model
; J. Comp. Chem. 16(4), 501-511 (1995)
;
; Possible defines that you can put in your topol.top:
; -DANISOTROPIC Select anisotropic polarizibility (isotropic is default).
; -DRIGID Rigid model (flexible is default)
; -DPOSRES Position restrain oxygen atoms
;
[ defaults ]
LJ Geometric
[ atomtypes ]
;name mass charge ptype c6 c12
WO 15.99940 0.0 A 0.0 0.0
WH 1.00800 0.0 A 0.0 0.0
WS 0.0 0.0 S 0.0 0.0
WD 0.0 0.0 D 0.0 0.0
[ nonbond_params ]
#ifdef RIGID
#ifdef ANISOTROPIC
WH WH 1 4.0e-5 4.0e-8
WS WO 1 1.0e-6 1.0e-12
WS WH 1 4.0e-5 2.766e-08
WO WO 1 2.0e-3 1.174e-06
#else
WH WH 1 4.0e-5 4.0e-8
WS WO 1 1.0e-6 1.0e-12
WS WH 1 4.0e-5 2.769e-08
WO WO 1 2.0e-3 1.176e-06
#endif
#else
#ifdef ANISOTROPIC
WH WH 1 4.0e-5 4.0e-8
WS WO 1 1.0e-6 1.0e-12
WS WH 1 4.0e-5 2.910e-08
WO WO 1 2.0e-3 1.189e-06
#else
WH WH 1 4.0e-5 4.0e-8
WS WO 1 1.0e-6 1.0e-12
WS WH 1 4.0e-5 2.937e-08
WO WO 1 2.0e-3 1.187e-06
#endif
#endif
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; This is a the 'classical YAW' model, in which we do have the dummy.
;; The shell is attached to the dummy, in this case the gas-phase
;; quadrupole is correct. Water_pol routine can be used for this
;; model. This has four interaction sites.
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
[ moleculetype ]
; molname nrexcl
SW 2
[ atoms ]
; id at type res nr residu name at name cg nr charge
1 WO 1 SM2 OW1 1 1.24588
2 WH 1 SM2 HW2 1 0.62134
3 WH 1 SM2 HW3 1 0.62134
4 WD 1 SM2 DW 1 0.0
5 WS 1 SM2 SW 1 -2.48856
#ifdef ANISOTROPIC
[ water_polarization ]
; See notes above. Alphas in nm^3 (See ref. above)
; O H H D S funct al_x al_y al_z rOH rHH rOD
1 2 3 4 5 1 0.001415 0.001528 0.001468 0.09572 0.15139 0.0137408
#else
[ polarization ]
; See notes above. alpha (nm^3)
4 5 1 0.00147
#endif
#ifdef RIGID
[ settles ]
; i funct dOH dHH
1 1 0.09572 0.15139
#else
[ bonds ]
1 2 1 0.09572 458148.
1 3 1 0.09572 458148.
[ angles ]
; i j k
2 1 3 1 104.52 417.6
#endif
[ dummies3 ]
; The position of the dummies is computed as follows:
;
; O
;
; D
;
; H H
;
; 2 * b = distance (OD) / [ cos (angle(DOH)) * distance (OH) ]
; 0.0137408 nm / [ cos (104.52 / 2 deg) * 0.09572 nm ]
; 0.01557 nm
; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-X1)
;
; Dummy from funct a b
4 1 2 3 1 0.117265878 0.117265878
[ exclusions ]
; iatom excluded from interaction with i
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
#ifdef POSRES
; Restrain the oxygen...
[ position_restraints ]
; iatom type fx fy fz
1 1 100 100 100
#endif
=======================================
--
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
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