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

[Justin A. Lemkul]

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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