Hi. You should use the following command to center your protein: trjconv -f trajectory.xtc -o corrected_trajectory.xtc -pbc mol -center -s trajectory.tpr Don't forget to replace "trajectory" with corresponding filenames
2013/10/16 Shima Arasteh <shima_arasteh2...@yahoo.com> > > > Dear gmx users, > > I have a system consist of a lipid bilayer and a peptide. As the initial > configuration, the peptide is located in center of the x-y plane above > lipid bilayer. After running MD, the peptide shows interactions with the > polar groups. It's ok, but the peptide is near one edge of the x-y plane of > the bilayer. I' d like to know if there is any way to use the properties of > the pbc and see the peptide in center of the x-y plane while interacting > with the polar groups? > > Thanks in advance, > Your suggestions would be appreciated. > > Sincerely, > Shima > -- > 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 > -- Andrew Gonchar Андрей Гончар -- 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
