[gmx-users] shell model

[David van der Spoel]

abhishek sharma wrote:
> sir,
> 
>   i want to introduce a shell model in ZnS particles and have the 
> potential data. I gone through your Novel Shell Model for the water 
> molecule givem in the /share/top as sw.itp.
> 

> 
> could you please help me out how I can introduce all these potentials
> in my model I have the following data.
> 
> Species                                    Charge e
>    Zn core                                   +2.00
>    Cd core                                     +2.00
>    S core                                    +1.03061
>    S shell                                 −3.03061
>                                                                         
>    C eV/ Å6
>                                                                   Å     
>                  Cut-off Å
> Buckingham potential                         A eV
>    Zn core - S shell                        672.288     0.39089      
> 0.0     12.00
>    Cd core - S shell                       1240.9518    0.371852     
> 0.0     12.00
>    S shell - S shell                           1200.0     0.14900      
> 0.0     12.00
>                                              k eV/ Å2
>    Core-shell potential                                 Cut-off Å
>    S core - S shell                        13.302743       0.8
>                                           k eV/ rad2
> Three-body potential                                          °    1/ 2  
> Å Cut-off Å
>                                                            0
>                                                     106
>    S shell - Zn core - S shell           9.42834         109.47      
> 0.3       6.0
>                                                     107
>    S shell - Cd core - S shell           3.59468         109.47      
> 0.3       6.0
> Torsional potential                          kt eV        m/n      rmin 
> Å   rmax Å
>    Zn core - S shell - Zn core - S shell     0.005       +1 / + 3    
> 2.5       3.0
> 
> 
I would urge you to read chapters 4 and 5 of the manual.

Are these Buckingham potentials for next neighbors as well?  Most likely 
  not, but in that case you need some kind of bond potential.

Anyway, if this system is completely non-bonded then it becomes a bit 
more difficult since there are no non-bonded three body interactions 
implemented. In that case you need to make a tabulated bonded potential, 
for each of the different interactions involved in direct bonds. You can 
probably use x2top to generate a topology file for your system, but yu 
will have to make your own .n2t input file for it. Check the existing 
ffoplsaa.n2t file for reference.



-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se