[gmx-users] SWM4-NDP or SWM4-DP water model is needed.

[zhongjin]

Dear GMX users:
I want to simulate water with polarizable water molecule models? I am not clear about how to construct the itp files for them. I have seen swm-dp.itp on http://lists.gromacs.org/pipermail/gmx-users/2006-August/023476.html
; 
; Topology file for SSWM4-DP
;
; G. Lamoureux, A. D. MacKerell, Jr., B. Roux
; A simple polarizable model of water based on classical Drude oscillators
; J. Chem. Phys.,  119 (5185-5197), 2003
;
; Possible defines that you can put in your topol.top:
; -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 ]
WO      WO      1       3.561658e-03	3.685198e-06

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; 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      -1.77185
2	WH	1	SM2		HW2		1	0.55370
3	WH	1	SM2		HW3		1	0.55370
4	WD	1	SM2		DW		1      -1.10740
5	WS	1	SM2		SW		1       1.77185

[ polarization ]
; See notes above.	alpha (nm^3)
1	5	1 	0.00104252

;[ settles ]
; i	funct	dOH	dHH
;1	1	0.1	0.16333

[ constraints ]
; i     funct   doh     dhh
1       2       1       0.09572
1       3       1       0.09572
3       2       1       0.15139

[ 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	0.2031807494	0.2031807494

[ 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

But I think:
[ constraints ]
; i     funct   doh     dhh
1       2       1       0.09572
1       3       1       0.09572
3       2       1       0.15139

conflict with

;[ settles ]
; i funct dOH dHH
;1 1 0.1 0.16333

I think it should use 
;[ settles ]
; i funct dOH dHH
;1 1 0.09572  0.15139

 
Anybody could give some helps?
 
Thanks a lot!!!
 
Zhongjin He
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