Hello, I had success with membrane simulations with:
1) -pbc nojump 2) -center 3) -pbc mol 4) -fit rot+trans This usually works to have the protein fitted and centered. Best regards, Marlon Sidore PhD Student Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) CNRS - UMR7255 31, Chemin Joseph Aiguier 13402 cedex 20 Marseille France 2017-02-22 8:57 GMT+01:00 Мижээ Батсайхан <b.mijidd...@gmail.com>: > Dear gmx user, > > Hello, I complited calculation of KALP15 in DPPC. I would like to make > further analysis such as generate structures of trajectory. > I used following sequence of commands for gmx trjconv: > > 1. -pbc nojump > 2. -pbc mol -ur compact > 3. -pbc res (one case, ignored, but result is same) > 4. -fit transxy > > In the result, there are some atoms of water very far from the system. > How can I get right structure view? > Please advice me? > Is there any common used sequence of trjconv's command this type of > situation? > > Best regards, > Mije > -- > 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.
