[gmx-users] RDF of a group around CNT axis
Sajjad Kavyani
kavyani.sajjad at gmail.com
Wed Jun 7 15:42:14 CEST 2017
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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