At first, I gave, gmx trjconv -pbc whole -s prd.tpr -f prd.xtc -o trajwhole.xtc I selected "system" for output
It says Program gmx trjconv, VERSION 5.1.4 Source code file: /cygdrive/d/software/GROMACS/gromacs-5.1.4/src/gromacs/gmxana/gmx_trjconv.c, line: 1322 Fatal error: Index[6376] 6377 is larger than the number of atoms in the trajectory file (6376). There is a mismatch in the contents of your -f, -s and/or -n files. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- Which index number should I select for all the three commands mentioned above? Thanks, Neha On Sat, Dec 30, 2017 at 9:42 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 12/30/17 10:47 AM, Alexandr Nasedkin wrote: > >> gmx trjconv -s prd.tpr -f trajwhole.xtc -pbc nojump -o trajclust.xtc -n >> index.ndx -center >> >> > Removing jumps and centering simultaneously should be considered mutually > exclusive. One usually needs a few rounds of trjconv, e.g. > > gmx trjconv -pbc whole > gmx trjconv -pbc nojump > gmx trjconv -pbc mol -center > > Almost always does the trick for simple systems. > > -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.