[gmx-users] Graphene - force field

[Mark Abraham]

On 13/01/2012 2:22 PM, Nilesh Dhumal wrote:
> 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

You need to choose some actual values here, not comment them out.

> ; 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

You should look at some example .rtp entries. You need to give a unique 
name to each atom, and to describe which are bound to which.

Chapter 5 is your friend, read its examples.

Mark

>
>
> 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
>
>