Hi Victor, With 'pbc whole' polymer remains broken in pbc and the octahedron box looks weird too.
JIom On Thu, Oct 1, 2015 at 2:52 PM, Victor Rosas Garcia <rosas.vic...@gmail.com> wrote: > Have you tried the option "-pbc whole" instead of "-pbc mol"? > > Victor > > 2015-10-01 6:43 GMT-05:00 gromacs query <gromacsqu...@gmail.com>: > > > Hi All, > > > > I have linear polymer in octahedron box and when I try to visualise a > > polymer in octahedraon box then water octahedron box looks as expected > but > > my polymer looks broken. > > > > trjconv_avx -f input.xtc -o out.xtc -pbc mol -ur compact -s input.tpr -b > > 100000 > > > > I have tried to use -center (whole polymer selection) also but still it > > looks broken. > > > > I want to write some pdbs for some analysis and this way my polymer is > > broken in pbc. > > > > Thanks for any suggestions. > > JIom > > -- > > 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.