--- On Tue, 19/2/13, Justin Lemkul <[email protected]> wrote: > First use: > > trjconv -trans x y z -pbc mol > > This will allow you to reposition the elements of your > system such that you have an intact structure at the > origin. Then use the structure created as your new > reference structure for further trjconv iterations (removing > jumps, making molecules whole, etc).
Thank you, but I must be doing something wrong. With -trans x y z -pbc mol the broken molecule is indeed displaced out of the origin, but it remains broken, and further runs of trjconv (passing this new structure with -s or -f) don't seem to help. I've tried attaching sample files, but the list doesn't like that. For the record, I've since noticed that -pbc cluster works in gromacs 4.5.5, but not in 4.5.3, so in a machine with the former this appears to work: $ trjconv -f final.gro -s init.tpr -o tmp.gro -pbc cluster (select group 2 for clustering) $ trjconv -f tmp.gro -s init.tpr -o new.gro -pbc mol -center -boxcenter zero -ur compact (select group 2 for centering) And my newest finding is that if I define bonds inside the frozen molecule, then I can do without the "-pbc cluster", and just a single "-pbc mol -center -boxcenter zero -ur compact" does what I need, and it joins together in the center the frozen molecule that was initially broken. So, where I would normally just use (simplified case, real case is more complex): [atoms] 1 opls_111 1 SOL OW 1 -0.834 2 opls_112 1 SOL HW1 1 0.417 3 opls_112 1 SOL HW2 1 0.417 [exclusions] 1 2 3 2 3 it's better to add: [bonds] ; type "5" is a dummy bond 1 2 5 1 3 5 -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
