So I've removed pbc from the structure and defined new box dims by editconf. Now how I could cut all atoms which are not inclluded to that box ( water in upper and lower leaflets) ? As I told when I did it by means of genbox -cs b2ar_Smaller.gro -box 8.68740 8.41864 9.70145 atom order of the protein have been perturbed.
James 2012/12/21 James Starlight <jmsstarli...@gmail.com>: > Hi Tsjerk! > > 1-Could the hexagonal prism be used with the membrane contained system > ? Could you show me visual example of such pbc for bilayer-like > systems ? > > 2-Have GROMACS build-in utilities for such deletion of the atoms > within specified cut-offs ( e.g above or below specified distanses) > > James > > 2012/12/21 Tsjerk Wassenaar <tsje...@gmail.com>: >> Tsjerk -- 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
