[gmx-users] Re: help with improper angle in gmx (Justin Lemkul)

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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