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
--
========================================
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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