[gmx-users] rdf

shakuntala dhurua madhu.dhurua94 at gmail.com
Sun Nov 10 15:19:41 CET 2019


Thank you Justin I will follow
On Sun, 10 Nov 2019, 7:05 pm Justin Lemkul, <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
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> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
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