Hello, I am trying to build a bigger liquid phase (1000) from a small cluster of molecules (125). So far I have succeeded in forming the small cluster of 125 molecules shown in the below image. This was after running gmx trjconv ... -pbc cluster -center to bring the molecules into the middle of the box.
http://i.imgur.com/nlgDUzh.png Now, the seemingly very trivial issue I am having is that I cannot figure out how to remove the empty space surrounding the cluster. I would like to do this automatically rather than by manually specifying a box size. Can anyone suggest a workflow for doing this? Thanks, John -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
