Dear Justin, you’re right. The problem was the system was not center properly in the initial .gro file. Now it works.
Thank you very much. Juan C. On 5/17/14, 5:49 AM, Juan Munoz-Garcia wrote: > Dear Mark, > > I’ve used numbers. Just indicated them as x_box/2, etc to be clearer. > There are two possibilities: 1. You built the system wrong and trjconv can't fix it. Without the full sequence of commands used to build the system, no one can provide any advice here. Providing an image that shows the unit cell ("pbc box" in the Tcl window in VMD) can also be informative in this regard. 2. This is a PBC issue that should be resolvable, probably within a few iterations of trjconv. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow. Often times, it helps to start with a new .tpr file that has the system centered properly when remove jumps, etc. -- 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.