[gmx-users] Re: question about dihedral angle in *.itp file
mark.abraham at anu.edu.au
Mon Jan 8 07:58:59 CET 2007
> Thank you very much for your answer!
> I have check manual in chapter4. I am still confused about this sentence.
Which sentence? Please either quote it, or refer precisely to it with a
reference. Nobody is going to read the whole of chapter 4 to find the one
relevant sentence that is confusing you :-)
> As we know, each dihedral was counted only once(?) in the program.
> if several torsional dihedral angles with different parameters can be
> on the same set of atoms i, j, k, and l, does this mean that this dihedral
> be counted several times.
For purposes of GROMACS, a bonded function is defined by the function type
(an integer) and the set of atoms to which it applies. See table 5.4.
There may only be one instance of a given function type for a given set of
atoms. grompp will take the last such function that it finds. Thus you
cannot have multiple periodic dihedral functions on the same four atoms,
even if their multiplicity varies.
> for second question about multiplicity m
> i am really confused about the physical mean of m, according to equation
> it seems that m is just the periodiocity of Cosine function.
> Could anyone help me figure out, Thank you very much:)
That equation didn't come from the gromacs manual as far as I can see.
"multiplicity" and "periodicity" are referring to the same phenomenon -
that of the rate with which the sinusoid repeats itself. m determines the
number of minima the function has - the multiplicity. Thus for a H-C-C-H
dihedral you would want minima every 120 degrees, but for H-C=C-H every
180 degrees. The simplest functional form that will do both of these is a
sinusoid with a periodicity/multiplicity parameter. The derivation of the
word is from "multiple" in reference to a quantity, rather than "multiply"
the operation, if that helps.
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