[gmx-users] Re: help with improper angle in gmx (Justin Lemkul)
jalemkul at vt.edu
Tue Jan 8 18:14:13 CET 2013
On 1/8/13 12:06 PM, Tom wrote:
> Table 5.5 does list the option of use harmonic type potential for improper
> dihedral. (f. tp =5)
It's function type 2.
> But I am confused how to build this on the ffbond.itp file and manu is not clear
> about this.
You would define the interaction in ffbonded.itp in a [dihedraltypes] directive
and specify the four atoms involved in addition to a force constant and
equilibrium value. In the .top, you would list the four atoms (by number) in a
[dihedrals] directive, followed by function type 2.
> Do you think that in the case of OPLS AA, the periodic improper dihedral is the
> ONLY option?
It is. Those impropers are built into the force field, which assumes the usage
of a certain functional form for these interactions. If you want harmonic
impropers, you shouldn't be using OPLS.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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