Hello GROMACS users, I have created an infinite liquid film system by building a slab of molecules in a 3D periodic unit cell where two dimensions of the film (x and y) extend out to the edge of the unit cell and one (z) does not.
I found the slab drifts along the z-dimension during MD and I am trying to post-process the trajectories to anchor the slab in the center of the unit cell. "trjconv -pbc mol -center -boxcenter" works well for most trajectories *unless* the slab drifts so much that it comes in contact with the z boundary. When this occurs, "trjconv -pbc mol -center -boxcenter" anchors it in a different location. Any ideas how I can anchor the system to the center of the unit cell in this situation? Best, Eric -- 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.
