Hi, I think its solved, I used -center option but now rather selecting full polymer I selected some of the central residue in polymer chain. Now box looks good and polymer is not broken.
JIom On Thu, Oct 1, 2015 at 3:43 PM, gromacs query <gromacsqu...@gmail.com> wrote: > 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.
