compute rdf for center of mass

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1

I would like to compute the radial distribution function (RDF) between similar molecules of higher alkanes such as aliphatic n-C22.

For example, to represent the center of mass for this hydrocarbon, I would like to specify the 11th carbon on this chain as the atom type for the RDF calculation. My problem is all the Carbon atoms in n-C22 are of the same atom type. Is there a way to compute RDF between certain atoms on a chain of atoms with the same atom type?

Thanks,

J. Berry

2

I would like to compute the radial distribution function (RDF) between
similar molecules of higher alkanes such as aliphatic n-C22.

For example, to represent the center of mass for this hydrocarbon, I would
like to specify the 11th carbon on this chain as the atom type for the RDF
calculation. My problem is all the Carbon atoms in n-C22 are of the same
atom type. Is there a way to compute RDF between certain atoms on a chain of
atoms with the same atom type?

the simplest approach would be to simply give the 11th carbon a
different atom type number, but use the same parameters as for the
other carbons of the same type.

axel.