Bumping this once before the weekend, hoping to get some help. I am getting segmentation fault errors at 1 to 2 million cycles into my production MD runs, using GROMACS 4.5.4. If these errors are a consequence of a poorly-equilibrated system, I am no longer getting the right kind of error messages to support that conclusion. I am not getting PME or SETTLE errors. I am getting a non-descriptive segmentation fault.
I have corrected earlier shortcomings in my equilibration protocols, as discussed in this earlier thread: http://gromacs.5086.n6.nabble.com/Re-Water-molecules-cannot-be-settled-why-tp4999302.html I am now monitoring the macroscopic properties of my simulation. Potential, pressure, density, and temperature convergence and subsequent stability are achieved, at least as well as demonstrated in Justin Lemkul's most recent tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html The trajectories of my simulations do not appear to be radical in any way that I can discern. I have a partially-unfolded protein, folding gradually, in a box of water with counter-ions. >From my previous thread, I have come to appreciate just how far from equilibrium the initial state of a simulation can be. Also, I have always understood that MD simulations are chaotic, and that instabilities can result simply from the fact that a continuous system is being modeled in discrete time steps. (As an aside, one of my first programming puzzles was about exactly this kind of thing. When I was a high-school student, I wanted to simulate the orbits of the Moon about the Earth, and the Earth about the Sun. It sounded simple enough, just apply the inverse-square law for gravity, right? Yet no matter how I tried, I couldn't achieve a stable system. Deeper reading led me to the intuitive and quick "leapfrog" method of improving differential approximations, which GROMACS apparently uses: and the more powerful but slower Runge-Kutta methods, which GROMACS apparently does not use.) By correcting my earlier problems, I have extended the time that my simulations will run by a factor of 10-20 fold, out to several nanoseconds. That's progress, but I'm never going to get to one microsecond this way. Any advice is appreciated. Of course I can post MDP files again, as well as graphs. -- View this message in context: http://gromacs.5086.n6.nabble.com/Segmentation-fault-mdrun-mpi-tp5001601p5001705.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
