On Thu, Oct 27, 2011 at 6:11 PM, Marzinek, Jan <j.marzine...@imperial.ac.uk> wrote: > > ________________________________________ > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf > of lina [lina.lastn...@gmail.com] > Sent: Thursday, October 27, 2011 10:47 AM > To: Discussion list for GROMACS users > Subject: [gmx-users] trjconv and -pbc > > 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, > > > > I am sure it will help. Follow the workflow! > > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions?highlight=pbc > > Just use the trjconv -h to see each option.
Ha, I think I have tried those options. That's why I am confused. Thanks, > > Jan > > =========================================================== > Jan Marzinek > PhD Candidate > Centre for Process Systems Engineering > Department of Chemical Engineering > Imperial College London > South Kensington Campus > London SW7 2AZ > E: j.marzine...@imperial.ac.uk > M: +44(0)7411 640 552 > > > -- > 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