Hi all, I have a simulation with a frozen molecule which stays around the origin, and a number of solvent molecules with pbc. Due to the way the simulation cell is defined, with a corner at the origin, by default my frozen molecule appears broken, a piece on every corner of the box, and I want it whole (and if possible centered).
In a simple world, I'd use trjconv with -pbc res (or mol) and -center, but of course, that doesn't work when initially the molecule is broken, as its center of mass is in a meaningless position. I can use -pbc atom, but then the solvent molecules get broken. So I assume I have to use a multi-step conversion, and I have to first get a whole molecule. But I tried -pbc whole and -pbc cluster and they don't make any difference. I can't find anything that works reliably, can anybody help me? Thank you Ignacio -- 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
