Hi Nilesh, To center the solute with respect to the solvent, first center the solute in the box, and then put the solvent in the box. Mind that that involves two passes of trjconv.
If 'no pbc effect' means no wrapping over the boundaries, yes you can use -dump with -pbc nojump to save a snapshot. trjconv will go over the frames and 'unwrap' the frames before the snapshot you want. Hope it helps, Tsjerk On Mon, Oct 17, 2011 at 9:18 PM, Nilesh Dhumal <ndhu...@andrew.cmu.edu> wrote: > Ya, I want to center solute w.r.t to the solvent. > > I have more question, if I want to save the coordinates of a snapshot with > no pbc effect, can I use -pbc nojump in trjconv. > > nilesh > > On Mon, October 17, 2011 1:34 pm, Tsjerk Wassenaar wrote: >> Hey :) >> >> >> The reference plays no role in centering. But I guess that Nilesh expects >> centering of the solute w.r.t. to the solvent, or is looking at the >> wrong center (tric/rect). >> >> Cheers, >> >> >> Tsjerk >> >> >> On Oct 17, 2011 7:06 PM, "Justin A. Lemkul" <jalem...@vt.edu> wrote: >> >> >> Nilesh Dhumal wrote: > > Thanks Justin, > > Still solute is not at >> center. > >> >> Is your reference frame (i.e. the .tpr file) centered? If not, centering >> likely won't work as desired. I assumed that it was centered, per >> normal system building procedures. >> >> -Justin >> >> >>> Nilesh > > > On Mon, October 17, 2011 11:27 am, Justin A. Lemkul wrote: >>> > >>> >>>> Nilesh Dhumal wrote... >>>> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read >> http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
