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.
