[gmx-users] Lennard-Jones Parameters in ffnonbonded.itp
Mark.Abraham at anu.edu.au
Mon Feb 20 18:51:28 CET 2012
On 21/02/2012 4:36 AM, Lara Bunte wrote:
> 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
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