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 _______________________________________________ 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
