[gmx-users] CNT in water

[Vitaly V. Chaban]

See [nonbond_params] topology section, I guess...




On Sun, Sep 27, 2015 at 6:18 PM, maryam haji <maryam6890 at gmail.com> wrote:

> Dear Users,
>
> I want to simulate CNT in water solvent with CHARMM27 force field. The used
> parameters for simulation of CNT follows:
>
>
>
> The .n2t file is:
>
>
>
> C    CA    0.00    12.011  3    C 0.141   C 0.141   C 0.141
>
> C    CA    0.00    12.011  2    C 0.141   C 0.141
>
>
>
> The cntbonded.itp is:
>
> [ bondtypes ]
>
> ; i         j           func     b0        kb
>
> CA  CA           3          0.1418   47890.0   21.867
>
>
>
> [ angletypes ]
>
> ; i         j           k          func     th0       cth       ub0
> cub
>
> CA      CA      CA      2          120.00 562.20
>
>
>
> [ dihedraltypes ]
>
> ; i         j           k          l           func     phi0     cp
> mult
>
> CA      CA      CA      CA      5  0.00 25.12 0.00 0.00
>
> The cntnonbonded.itp is:
>
> [ atomtypes ]
>
> name    at.num mass    charge  ptype   sigma   epsi
>
> CA      6          12.01100         0.00     A         0.385   0.4396
>
>
>
>
>
>
>
>
>
> The flexible SPC water model is used for simulation of water. The used
> parameters for simulation of water are (spc_cnt.itp):
>
>
>
> [ moleculetype ]
>
> molname          nrexcl
>
> SOL                2
>
> [ atoms ]
>
>      nr   type  resnr residue  atom   cgnr     charge       mass
>
>      1     OW   1    SOL     OW      1      -0.82
>
>      2     HW   1    SOL    HW1      1       0.41
>
>      3     HW   1    SOL    HW2      1       0.41
>
>
>
> #ifndef FLEXIBLE
>
> [ settles ]
>
> OW     funct    doh      dhh
>
> 1          1          0.1       0.16330
>
>
>
> [ exclusions ]
>
> 1          2          3
>
> 2          1          3
>
> 3          1          2
>
> #else
>
> [ bonds ]
>
>  i          j           funct    length  force.c.
>
> 1          2          1          0.1       463700            0.1     463700
>
> 1          3          1          0.1       463700            0.1     463700
>
>
>
> [ angles ]
>
>  i          j           k          funct    angle    force.c.
>
> 2          1          3          1          109.47 383      109.47 383
>
> #endif
>
> I have a question:
>
> I don’t know how to use the parameters of the Lennard-Jones potential, ɛCO
> and *σ*CO for calculating interaction between water molecules and carbon in
> nanotube in this simulation?
>
>
>
> Thank you for any help
> --
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