Hi, If it was something fundamentally wrong, you'd see an issue before this. Martini is just inherently a teensy bit unstable - but this is where the non-reproducibility of simulations comes in handy; restarting from far enough away will likely avoid a transiently high energy event.
Kevin On Tue, Feb 26, 2019 at 4:57 AM zeineb SI CHAIB <zeineb...@hotmail.com> wrote: > Dear Kevin, > > Thank you for your reply. > > I did 2 tests: > 1- I wanted to see in details when the system crashes and which atoms are > involved so I restarted the simulation from the checkpoint but using a new > mdp file. The only parameter that I changed was nstxout-compressed = 1. In > this case, the simulation didn't crash. > The command lines that I used were: > gmx grompp -f md_2.mdp -c npt.gro -p topol.top -n index.ndx -o md_2.tpr > gmx mdrun -deffnm md_2 -cpi md.cpt -noappend -nt 1 > > 2- I restarted the simulation from the same checkpoint as in (1), using > the first mdp file (with nstxout-compressed = 1000) and the simulation > crashed again at the same step. > The command line that I used were: > gmx mdrun -deffnm md -cpi md.cpt -noappend -nt 1 > > I compared the log files of (1) and (2) and it's starting from the same > time/steps but as I said (1) didn't crash and (2) crashed. > > I can restart the simulation with the new mdp file and keep it running > again but I want to be sure that It's a random crash and it is not a sign > of something more fundamentally wrong (physically unrealistic) with my > system. > > Zeineb > > > -- > Gromacs Users mailing list > > * Please search the archive at > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&data=02%7C01%7Ckevin.boyd%40uconn.edu%7C1f38b091b8c643b55beb08d69bd0e0b5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636867718780368928&sdata=cRy2XaqophqHtri3oM1ULmutD4SkyOahI8ciWmRmdIw%3D&reserved=0 > before posting! > > * Can't post? Read > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists&data=02%7C01%7Ckevin.boyd%40uconn.edu%7C1f38b091b8c643b55beb08d69bd0e0b5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636867718780378938&sdata=zhoh9PJa1GBu41GleQ9KQ5CKgbZeNO0X6fS0pkDnV%2F8%3D&reserved=0 > > * For (un)subscribe requests visit > > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-users&data=02%7C01%7Ckevin.boyd%40uconn.edu%7C1f38b091b8c643b55beb08d69bd0e0b5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636867718780378938&sdata=yXVlFuucw%2FqadP%2FOQKc0SLVPGBtOygkiGKZWwnEHsTI%3D&reserved=0 > or send a mail to gmx-users-requ...@gromacs.org. > -- 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.