The artifacts warning is general (mentioned in the manual) and has nothing to do with your system (aside from your mdp), everyone using absolute reference frame gets this warning.
That said, the error you're getting is actually descriptive. So: 1. Check if the system is stable and happy without pulling. 2. Make sure the pulling rate is compatible with your nstlist setting. If the neighbor list update rate can't keep up with your pulling rate, that's a problem. High pulling rates in thermostatted systems are also generally problematic from the physical standpoint. Severely problematic. Steered MD is to be carefully designed. 3. Make sure your boundaries are taken care of properly, in case your pulled object meets the wall. Alex hy> Hello all, hy> Recently, I preformed a SMD, pulling a nano diamond across the membrane. I hy> found that pull_geometry position in the Gromacs 4.6.5 (suggested in the hy> tips of the US tutorial by Justin.A ) was replaced by pulling with absolute hy> reference point in Gromacs 5.0.2. After defined pulling parameters hy> according to the manual, Gromacs gave me a warning that "This will lead to hy> artifacts". I really want to know what did it mean, so I ignored it by hy> using maxwarn 1 and saw what would happen. Finally I got a segment fault hy> that a bonded atom moved away, out of the cut-off distance. hy> Can you give me some advises? How can I treat the pulling correctly for hy> this penetrating process and why does the absolute reference lead to hy> artifacts. hy> Many thanks! hy> Hang -- 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.