[gmx-users] Lennard-Jones Parameters in ffnonbonded.itp

[Mark Abraham]

On 21/02/2012 4:36 AM, Lara Bunte wrote:
>
> Hello
> I use a charmm force field in gromacs. I almost finished my parametrization except for Lennard-Jones parameters. For this parameters I want to adopt the values in the charmm force field for the basic atom types.
>
> In gromacs I have to put this parameters in the ffnonbonded.itp file in the section [ pairtypes ] and I have to give following informations:
>
> ; i     j       func    sigma1-4        epsilon1-4 ; THESE ARE 1-4 INTERACTIONS
>
> in example
>
> CP1     CP1     1       0.338541512893  0.04184
>
> Now here is a section of information given in the charmm documentation.
>
> !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
> !
> !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
> !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
> !
> !atom  ignored    epsilon      Rmin/2   ignored   eps,1-4       Rmin/2,1-4
> !
> HN1      0.0       -0.0460    0.2245
> HN2      0.0       -0.0460    0.2245

Sometimes CHARMM has special values for 1-4 interactions of some atom 
types (in the last two columns) and sometimes not. CHARMM computes the 
actual interaction parameters in the program. GROMACS has pre-computed 
these in the [ pairtypes ] according to the combination rule. IIRC 
there's some redundant entries where neither atom type has special 1-4 
interactions. See manual 4.1.1 and 5.3.2 for how GROMACS needs these 
computations to work.

>
>
> The question is:
>
>
> How to adopt the values in the charmm force field for the basic atom types in gromacs? I do not really know what I have to write in the [ pairtypes ] section in gromacs.

What's wrong with the existing contents of 
$GMXLIB/share/top/charmm27.ff/ffnonbonded.itp?

Mark