[gmx-users] rdf calculation for wormlike micelles

Joe Jordan e.jjordan12 at gmail.com
Thu Mar 15 10:41:02 CET 2018

You cannot use a line as the reference. From a brief glance at the paper
you link it seems like maybe you actually want to compute the expectation
value of the micelle backbone, a method known as principle curves which is
a generalization of principle component analysis. At any rate, you should
probably just follow whatever procedure they use in the paper you are

On Thu, Mar 15, 2018 at 7:48 AM, Esra Kaçar <esrakacar at iyte.edu.tr> wrote:

> Dear Joe,
> Sorry for the confusion. I am working with martini force field and I have
> three different molecules in the micelle structure. I want to analyze the
> RDF of the constituent molecules with respect to the line that pass through
> the center along with its length. As I mention before this line has a
> curved structure and I couldn’t figure out how to select that line as a
> reference point. I guess a picture would be more helpful to explain my
> purpose. It is similar to the Figure 3 in the paper that I gave the link
> below:
> https://pubs.acs.org/doi/10.1021/acs.langmuir.7b01176
> Many thanks,
> Esra
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Joe Jordan

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