[gmx-users] some puzzled about the dihedral paramaters

Mark Abraham Mark.Abraham at anu.edu.au
Mon May 25 16:13:10 CEST 2009

Jinyao Wang wrote:
> gmx-users,
>  Dear all,
>   I make a *.itp for benzene by myself. All parameters come from the
> ffoplsaabon.itp and ffoplsaanb.itp. while I have some puzzled about the
> dihedral parameters of benzene.

You should check out the literature of OPLS/AA and see how aromatic
rings are intended to be treated. Basically, if you're using improper
dihedrals to enforce planarity, you probably don't want any other
dihedral potentials.

> In ffoplsaabon.itp file, there are
> dihedral parameters of benzene and the potential function is 3, like
> this:
> ;X CA CA X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> aromatic ring

The semicolons make this whole line a comment, which is consistent with
not wanting both proper and improper dihedrals here.

> but for improper dihedral of benzene there is some another dihedral
> parameters of benzene and the potential function is 1,like this:
> ; Z -CA-X -Y improper torsion. CA is any ring carbon
> #define improper_Z_CA_X_Y 1 180.0 4.60240 2
> I think the improper dihedral can keep the molecule of benzene planar.
> So I have no idea how to set dihedral the parameters of benzene. 

You won't be sure until you've read the primary literature.


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