I just experienced this myself. The problem appeared to manifest itself when I was using -mol on a molecule that straddled the box wall. Memory usage was extremely high and the resulting MSD plot did not show any linear behavior. Imaging the trajectory with -pbc nojump made g_msd's memory usage drop dramatically and produce a MSD plot more like what I would expect -- a linear region on the 10s of ns scale bookended by nonlinear regions. In this latter case, the results with and without -mol, though not numerically identical, are at least approximately equal. So, it looks like PBC handling may be at fault for one or both of the problems (memory usage and results with/without -mol) here.
Regardless of whether this is a bug or a natural consequence of trying to do a MSD calculation on broken molecules, the documentation for g_msd implies that g_msd handles periodic boundary conditions implicitly; perhaps the documentation should be updated to emphasize the (in hindsight, completely logical) fact that molecules need to be whole before running g_msd -mol. MZ -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
