Hi all, My simulation is composed of 2 protein chains wrapped around a lipid disk composed of a dozen different lipid types, water and ions in a 15nm cube. The protein encircles the mixed composition lipid disk. I've got 4 duplicate simulations with velocities generated from a different random seed. The starting structure for these simulations was taken from the end of a previous 200ns simulation (same settings but bigger box) which ended normally. I am using gromacs 4.6, with the gromos54a7 force field. No gpus.
The first simulation exploded (a few atoms fly off into the distance leaving the rest intact) shortly before 150ns, two more have crashed shortly before 200ns. 1 is still running. Restarting a simulation has it crash at a different point. Over 3 steps of escalating LINCS warnings I get a warning followed by a fatal error The atoms initially involved in the LINCS warnings correspond to atoms around a double bond in a single lipid tail. Specifically in linoleic and linolenic (2 or 3 double bonds in sequence). The parameters used were adapted from the packaged POPC parameters using the same bond types from ffbonded.itp Energy graphs seem to indicate that the system is equilibrated. Does anyone have any ideas what's going on here? Thanks in advance, -Trayder P.S. mdp file -- View this message in context: http://gromacs.5086.x6.nabble.com/Equilibrated-system-explodes-after-200ns-tp5007963.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
