[gmx-users] CNT in water

[Justin Lemkul]

On 9/27/15 5:18 PM, maryam haji 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):
>

Don't use flexible water models during dynamics, and don't use SPC with CHARMM. 
  It's fundamentally wrong.

>
>
> [ 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?
>

You don't need to do anything unless you want to override the normal combination 
rules.  In any case, check your assumptions, because what you've proposed here 
isn't physically valid.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================