Hi, Right, but genbox puts things inside the rectangular brick corresponding to the unit cell, starting at the origin. That means that if the solute is on one end, then placing something close to the part that sticks out will actually be put on the other side of the box. But maybe I just want to make it too simple :)
Cheers, Tsjerk On Thu, Aug 13, 2009 at 11:25 PM, Vitaly V. Chaban<vvcha...@gmail.com> wrote: > Tsjerk, > > I understood the situation in such a way that MD was not run at all, > so Jamie visualizes *gro* file obtained with *genbox*... > > Jamie, > didn't you look at this: http://www.ime.unicamp.br/~martinez/packmol/ > to prepare your system? > > > Vitaly > > >> >>> Thanks for the answer. When I said far away means my pore was in one corner >>> of vmd window and the water molecules in opposite corner (almost). >> >> Did I miss something or did neither Vitaly nor Justin reply "Are you >> perhaps seeing the effect of periodic boundary conditions?". >> >> Tsjerk >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> Junior UD (post-doc) >> Biomolecular NMR, Bijvoet Center >> Utrecht University >> Padualaan 8 >> 3584 CH Utrecht >> The Netherlands >> P: +31-30-2539931 >> F: +31-30-2537623 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ 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/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/mailing_lists/users.php
