No! You can't do that, because fitting will cause the PBC and the coordinates to mismatch. So 'nojump' after that will for sure screw up the coordinates. Check the trjconv workflow on the Gromacs site.
Cheers, Tsjerk On Mar 31, 2016 14:23, "Francesco Carbone" <fra.carbo...@gmail.com> wrote: > You could try to fit first (-fit rot+trans) and fix pbc (-pbc nojump) > later. > > Cheers, > > Fra > > On 31 March 2016 at 05:45, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > > > Hi Irem, > > > > Check the structure in nvt_water_frozen.tpr: > > > > gmx editconf -f nvt_water_frozen.tpr -o ref.pdb > > > > Cheers, > > > > Tsjerk > > On Mar 31, 2016 00:04, "Irem Altan" <irem.al...@duke.edu> wrote: > > > > > Hi, > > > > > > I am simulating a protein in its unit cell. I use the original .pdb > file > > > as an input, so the initial molecule is not fragmented. At the end of > the > > > simulation, I generate a .pdb file containing the trajectory of the > > protein > > > as follows: > > > > > > gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc > > > nojump -o prot.pdb > > > > > > Despite the fact that I use -pbc nojump, I still get all the > coordinates > > > wrapped into the unit cell, and therefore the protein fragmented. What > > > could be wrong? (I use GROMACS 5.1.2) > > > > > > Best, > > > Irem > > > -- > > > 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. > > > -- > 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.
