[gmx-users] rdf

[shakuntala dhurua]

sir, as i m beginner of gromacs i want to calculate rdf between o-o of
only  bulk water simulation, here i have generate xtc file using gmx rdf -n
index.ndx -s water5.tpr -f water5.trr -o water5.xtc ,after that for rdf
calculation i have used gmx rdf -n index.ndx -s  water5.tpr -f water5.xtc
-o rdf_water.xvg then
 the out put was like that
Available static index groups:
 Group  0 "System" (2709 atoms)
 Group  1 "Water" (2709 atoms)
 Group  2 "SOL" (2709 atoms)
 Group  3 "OW" (903 atoms)
Specify a selection for option 'ref'
(Reference selection for RDF computation):
(one per line, <enter> for status/groups, 'help' for help)
after putting group 3  it shows below

Selection '3' parsed
Available static index groups:Selection '3' parsed
Available static index groups:
 Group  0 "System" (2709 atoms)
 Group  1 "Water" (2709 atoms)
 Group  2 "SOL" (2709 atoms)
 Group  3 "OW" (903 atoms)
Specify any number of selections for option 'sel'
(Selections to compute RDFs for from the reference):
(one per line, <enter> for status/groups, 'help' for help, Ctrl-D to end)
> 3 (here i am selected group 3 again) and it again shows
Selection '3' parsed
what is this actually i am not able to understand please help me to solve
this.



On Sat, Nov 9, 2019 at 7:57 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/9/19 1:03 AM, shakuntala dhurua wrote:
> > I am facing proble while calculating rdf , after generating xtc file i
> used
> > flag gmx rdf -s .tpr -f .xtc -n .ndx -o .xvg then from index data i was
> > selected group1 and group2 but there it was written parsed group1 and
> > group2. please suggest me to solve this problem.
>
> Please provide the actual command and relevant screen output, including
> any error message. What you have posted doesn't even sound like an
> error. You chose two groups for a calculation, which were then parsed by
> the rdf program.
>
> -Justin
>
> --
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
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