Hi Justin, I got the same result as you said.
What confused me was, when I viewed movie.pdb file generated by the following command, gmx trjconv -pbc nojump -s PRD-SMP3.gro -f PRD-SMP3.xtc -e 10000.0 -n index.ndx -o movie.pdb two hydrogen molecules of my organic compound, were unbonded to my molecule (which is not supposed to be). They are far away from molecules (their bonds were broken) Is it a pbc problem? Because, when I used gmx trjconv -pbc whole -s PRD.tpr -f PRD.xtc -o trajwhole.xtc gmx trjconv -pbc nojump -s PRD.tpr -f trajwhole.xtc -o trajcluster.xtc gmx trjconv -pbc mol -center -s PRD.tpr -f trajcluster.xtc -o newtraj.xtc and created a .pdb file with newtraj.xtc, the whole molecule was intact. Thanks, Vidya.R On Sat, Jan 13, 2018 at 7:25 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/13/18 7:53 AM, Vidya R wrote: > >> Hi gmx users, >> >> I used the following commands after simulation run (organic compound in >> water, to calculate rdf) >> >> >> >> gmx trjconv -pbc whole -s PRD.tpr -f PRD.xtc -o trajwhole.xtc >> gmx trjconv -pbc nojump -s PRD.tpr -f trajwhole.xtc -o trajcluster.xtc >> gmx trjconv -pbc mol -center -s PRD.tpr -f trajcluster.xtc -o >> newtraj.xtc >> >> >> To use the following command, which xtc file should I use? >> >> gmx rdf -f ---.xtc -n index.ndx >> >> *prd or newtraj.xtc?* >> >> Please clear my doubt. >> > > Run both and see if there is a difference. gmx rdf should be PBC-aware, so > you should get the same result. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > > -- > 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.
