You mean if -pbc could make molecule whole,everything is ok, but if not it means the molecule was broken from first, yes?
Sent from my iPhone > On Jan 17, 2018, at 16:19, Justin Lemkul <jalem...@vt.edu> wrote: > > > >> On 1/17/18 5:51 AM, Vidya R wrote: >> 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. > > Making molecules whole should always be the first step. If you try to remove > jumps with "broken" molecules, what you visualize will be garbage. A separate > issue is with respect to the analysis programs - many are PBC-aware and can > handle the original trajectory without manipulation. > > -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.