[gmx-users] rdf calculation for wormlike micelles

[Joe Jordan]

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
citing.

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
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.




-- 
Joe Jordan