Have you tried pbc nojump or whole with trjconv? Sent from my iPhone
> On 02-Jul-2016, at 11:46 am, Seera Suryanarayana <paluso...@gmail.com> wrote: > > Dear gromacs users, > > I have simulated protein for 100ns. When I visualized the protein in VMD, I > have seen the protein into different fragments. Later I came to know that > there is no breaking phenomena in simulations and that is because of the > PBC problems. I have executed the trjconv command with following arguments > to solve the problem, but I couldn't make it successful. I also attached > the snapshot. Kindly guide me how to resolve problem? > > gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -center -pbc > mol -ur compact > > Surya > Graduate student > India. > -- > 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.
