On Fri, Oct 28, 2011 at 11:48 AM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi Lina, > > Make sure to use a reference in which the molecules are together (clustered) > the way you want them.
I used the initial mdrun .tpr. After checking the generated pdb (total 51 frames), the first 28/29 frames both are together, but later are separated. (the intra_fit also not work as expected). So I think at beginning the reference initial ones are together. This .xtc were trjcat together, first 200ns and then extend to 500ns, the .pdb generated used dt 10ns. > > Cheers, Am I wrong in some places? Actually for other trajectories I had no problem (use the same way of handling it). Thanks, > > Tsjerk > > On Oct 27, 2011 11:47 AM, "lina" <lina.lastn...@gmail.com> wrote: > > Hi, > > I have a problem using > > trjconv_g -pbc nojump > or > > trjconv_g -pbc nojump -center > > I even tried the -pbc whole. > > The system is protein with a small molecular, for the first time > period, when I checked on pymol. > they are together, but later they apart, after show cell, protein > inside the cell, while this small molecular outside, > > I did not meet such issue before, it's used to be easy to fix the pbc > problem, but not this one. a bit surprise, > > They are supposed to be together, > > Thanks for any advice, > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
