[gmx-users] rdf

[Justin Lemkul]

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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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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