[gmx-users] RDF of a group around CNT axis

[SRINIVAS MUSHNOORI]

If I understand you correctly: you want to calculate the RDF of a certain
group (NOT part of the nanotube) around the central axis of a nanotube?

The way I do these calculations is to use the gmx trjconv tool to isolate a
trajectory file of ONLY the gropus I am interested in and run my
calculations on that.
If you expect to see one peak but see many that might mean that the RDF is
picking up groups that you don't want it to.

Hope that helps,
Srinivas

On Wed, Jun 7, 2017 at 9:41 AM, Sajjad Kavyani <kavyani.sajjad at gmail.com>
wrote:

> Dear experts,
> I want to calculate rdf of a certain group around the axis of a cnt, but I
> do not know what are the proper parameters to choose in the command-line.
> To test the parameters, I calculated the rdf of cnt itself around its axis
> which must be a sharp peak at the cnt radius.
> I tested the following: (both selection groups of reference and rdf are
> CNT)
> gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos mol_com
> gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos res_com
> gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos whole_res_com
> gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos whole_mol_com
>
> BUT all the results are the same!!! and surprisingly they have multiple
> sharp peaks at different ranges, which I expected just one peak at the
> radius of the CNT !!!!
> It is notable that the CNT is aligned to z axis.
> (the first two peaks are listed below):
>
>       0.000 211939.438
>       0.002 53771.996
>       0.004 11278.401
>       0.006 3935.633
>       0.008 1782.280
>       0.010  809.616
>       0.012  584.723
>       0.014  536.531
>       0.016  292.361
>       0.018  149.929
>       0.020   94.455
>       0.022   00.000
>           ...
>           ...
>           ...
>       0.118    00.000
>       0.120    0.375
>       0.122    2.212
>       0.124    0.725
>       0.126    6.069
>       0.128   36.545
>       0.130  114.868
>       0.132  278.390
>       0.134 1669.916
>       0.136 2360.069
>       0.138  346.139
>       0.140  183.770
>       0.142   39.277
>
> Could you please explain to me that what should I do?
> --
> 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.
>