[gmx-users] CNT in water

[maryam haji]

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