zhongjin wrote:
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?
The [settles] directive is commented out and thus not used. Adjusting anything
on these lines has no effect. It certainly conflicts, but if the [constraints]
directive is used, it doesn't matter.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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