Hi, I am trying to solvate a small DNA molecule. Since I don't want so simulate more waters than what is really neccessary, I decided to try the dodecahdron and octahedron unit cells.
After I added waters I went to examine the resulting structures in VMD only to find that the octahedron and dodecahedron cells are completely wrong. Instead of the familiar shape (roughly a cube with trimmed edges for dodeachedron), I am greeted with a parallelepiped-like shape. I tried Gromacs 5.0.7, 5.1.3, 2016 but the results seem to be always the same. Is this an expected behaviour? How do I "reconstitute" the resulting structure? Thanks, Jernej -- 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.
