[gmx-users] Graphene - force field

[Nilesh Dhumal]

Hello,

I am trying to run simulation of graphene oxide.  I have 16 carbon atoms
of same type. I am using opls force field.  could make the .itp file and
pasted here

[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
;1               3               yes             0.5     0.5
; comb-rule 3 is square-root sigma, the OPLSAA version

[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name  bond_type    mass    charge   ptype          sigma      epsilon
opls_071  CG  6  12.01100  0.00   A  3.50000e-01 2.92880e-01
opls_072  CO  6  12.01100  0.265  A  3.50000e-01 3.59824e-01
opls_116  OH  8  15.99940 -0.683  A  3.12000e-01 7.11280e-01
opls_117  HO  1  1.00800   0.418  A  0.00000     0.00000


[ bondtypes ]
; i    j  func       b0          kb
  CO    OH      1    0.14100   133888.0
  OH    HO      1    0.09600   231375.0
  CG    CG      1    0.14000   392459.2   ; TRP,TYR,PHE
  CG    CO      1    0.14000   392459.2   ; TRP,TYR,PHE


[ angletypes ]
;  i    j    k  func       th0       cth
  CG     CO     OH      1    90.000    292.880
  CO     OH     HO      1   108.500    230.120
  CG     CG     CG      1   120.000    527.184      ; TYR(OL)


[ dihedraltypes ]
;  i    j    k    l   func     coefficients
; OPLS Fourier function (func=5)
CJ     CJ     CJ     CJ      3     30.33400   0.00000 -30.33400   0.00000 
 0.00000   0.00000 ;
  CG     CO     OH     HO      3      0.00000   0.00000   6.27600   0.00000
  CG     CG     CO     OH      3      7.15882  -2.09200   2.77399   0.00000

My question how can I step for the parameters ffoplsaa.rtp file. I made
the parameters as follow

 [ SMA  ]
 [ atoms ]
CG          opls_071     0.00       1
CG          opls_071     0.00       1
CG          opls_071     0.00       1
CG          opls_071     0.00       1
CO          opls_072     0.265      2
CG          opls_071     0.00       1
CG          opls_071     0.00       1
CO          opls_072     0.265      2
CG          opls_071     0.00       1
CG          opls_071     0.00       1
CG          opls_071     0.00       1
CG          opls_071     0.00       1
CG          opls_071     0.00       1
CG          opls_071     0.00       1
CG          opls_071     0.00       1
CG          opls_071     0.00       1
OH          opls_116    -0.683      3
HO          opls_117     0.000      4
OH          opls_116    -0.683      3
HO          opls_117     0.000      4

 [ bonds ]
    CG     CG
    CG     CO
    CO     OH
    OH     HO


I am geting trouble to create .top file using pdb2gmx.

Can you tell how to set up force field parameter for graphene.

I am usinng Gromacs  VERSION 4.0.7.

Thanks

Nilesh