Justin, thank you for reminding me that I need to adhere to sane parameters. I do have a few clarifying points, as it were. I tried these simulations again, but with a larger box and 0.9 nm cutoffs, and received a segfault at the same simulation time.
The model I am using, from the user contributed downloads section, does make use of virtual sites (virtual2). The choice for the masses and diatomic bond length always seemed strange to me (9 and 33 amu) b/c one could use almost identical masses. This would make setting up the virtual sites far more intuitive. I did this, after going through your tutorial for CO2, and this adaptation of the MeCN model suffers the same instability. I then took your CO2 model and modified it to CS2 using the proper LJ parameters from Madden's 1981 model that doesn't have charges. I ran this using coulombtype=cutoff and the 2 us simulation completed without any problems. I gave small (-0.01 for S and 0.02 for C) charges to the atoms and ran using PME, which crashed at 1.07 us. Do these results shed any new light on what is happening with my NPT simulations? -- View this message in context: http://gromacs.5086.n6.nabble.com/Diatomic-in-MeCN-NPT-NH-and-PR-simulation-segfaults-after-1-us-tp5001845p5002696.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
