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 <jalem...@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 > > -- > ================================================== > > 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 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.