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

[Sajjad Kavyani]

Dear Srinivas,
That's absolutely right, I want to calculate the RDF of a certain
group around the central axis of a nanotube.
And as I know that the RDF of the CNT around its axis is just a sharp peak
at the radius, I just tested the command-line parameters for this case, to
specify that which command-line should be used.

And honestly I do not understand the last sentence of your reply, could you
please specify that after isolating the desired group, what command-line I
should use?

Sincerely,
Sajjad



On Wed, Jun 7, 2017 at 6:54 PM, SRINIVAS MUSHNOORI <
scm177 at scarletmail.rutgers.edu> wrote:

> 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?
> > --
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