Hey Vito, After the first step, does the trajectory (say the last frame) look fine? If it does (everything nicely assembled), then after the second step, does it still look fine, and is it placed properly in the center of the box?
Cheers, Tsjerk On Wed, May 21, 2014 at 12:50 PM, Vito Genna <vito.ge...@iit.it> wrote: > Hi Tsierk, > > Ok. > > 1) trjconv_mpi -s em.tpr -f test.xtc -o test-nojump.xtc -pbc nojump > (output System) > > 2) trjconv_mpi -s em.tpr -f test-nojump.xtc -o test-center.xtc -center -n > index.ndx (centering all the frames on different targets Protein/DNA ecc > ecc) (output system) > > 3) trjconv_mpi -s em.tpr -f test-center.xtc -o test-compact.xtc -pbc mol > -ur rect[or compact] (output System) > > I also tried, successively, the same procedure adding one step more: -pbc > whole > This last step was added before the step 1. > > But at the end I obtain the same result. > > Surely, I'm doing something wrong but I'm not understand what is wrong...:/ > > Thank you for your time. > > V > > -- 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.
