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

[Sajjad Kavyani]

I noticed that the gmx rdf some how cannot find the center of mass (COM)
for the CNT because after that I manually put a single particle in the COM
of the CNT and calculated the rdf around it (with -xy option), the gmx rdf
resulted the expected value which is a sharp peak at the radius of the cnt.
I tested all the -selrpos arguments but none of them could find the COM of
the CNT
Could you please help me to manage the problem ?

Regards
Sajjad

On Wed, Jun 7, 2017 at 7:19 PM, Sajjad Kavyani <kavyani.sajjad at gmail.com>
wrote:

> 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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