On 11/9/19 11:17 PM, shakuntala dhurua wrote:
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.
It means the program is reading the group you chose. There's no problem
here. End your selection with Ctrl+D and the RDF will be computed.
-Justin
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