So I have spent the past few weeks debugging my equilibration protocols, which were an odd hybrid of examples ranging from GROMACS 3.3 up to GROMACS 4.5. I have cleaned out old code. I added an in vacuo energy minimization step for the protein without solvent, and a missing NVT step after solvent is defined. I have dimly grasped that, as long as you don't require compatibility with an older simulation, the V-rescale thermostat is the current recommended choice, and that switching thermostats (unlike barostats) can cause instabilities. I now know how to examine and graph macroscopic system parameters to assess stability. I think that everything should be looking good right now -- except that it isn't, not quite.
When I finally start the production MD runs, I have received two segmentation faults on two different test structures. They take a LONG time to appear -- over 1,070,000 iterations on one run, and over 2,360,000 iterations on another. On top of that, I'm not getting my usual error messages -- PME errors, or SETTLE errors. I'm not getting a dump of the last frame of my simulation. I had enough trouble accepting that my simulation parameters were set up incorrectly when I had failures 100,000 steps after starting the production MD run. Am I really supposed to believe that I still have instability problems? Here is the terminal output from one run (executing mdrun_mpi): Reading file test-prep.tpr, VERSION 4.5.4 (single precision) Making 1D domain decomposition 5 x 1 x 1 starting mdrun 'Protein t= 0.00000 in water' 2500000 steps, 5000.0 ps. [john-linux:09596] *** Process received signal *** [john-linux:09596] Signal: Segmentation fault (11) [john-linux:09596] Signal code: Address not mapped (1) [john-linux:09596] Failing at address: 0x3e950840 [john-linux:09596] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10060) [0x7f8a8ad5c060] [john-linux:09596] [ 1] /usr/lib/libgmx_mpi.openmpi.so.6(+0x1f9670) [0x7f8a8b413670] [john-linux:09596] *** End of error message *** -------------------------------------------------------------------------- mpirun noticed that process rank 2 with PID 9596 on node john-linux exited on signal 11 (Segmentation fault). -------------------------------------------------------------------------- The .log file does NOT contain any error messages, indicating any instability. The last entry in the log file is a long chain of energy status report blocks. Here's the last one: DD step 1078799 load imb.: force 1.8% Step Time Lambda 1078800 2157.60000 0.00000 Energies (kJ/mol) G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 2.07623e+03 8.42439e+02 6.03967e+02 -2.12322e+02 1.95589e+04 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 8.12766e+04 -9.12661e+02 -5.96406e+05 -4.40546e+04 -5.37227e+05 Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) 9.76293e+04 -4.39598e+05 3.10969e+02 -7.72781e+01 3.95185e+01 Constr. rmsd 1.90839e-05 I'm not a low-level programmer, and so I don't have to deal with this much, but... a segmentation fault generally indicates that a program is trying to write outside of its allocated memory block. The third line of the error message sent to the shell would seem to indicate exactly that. That doesn't actually sound like it has anything to do with my simulation being unstable. (However, with applications written in C, I'm willing to believe anything.) I did check on my memory usage. I have 8 GB of RAM on my system, running Ubuntu Linux 11.10, AMD 64-bit. At most, I'm using a bit more than half of my RAM (I have other, undemanding applications open besides my GROMACS terminal windows, and I also reserved one CPU core to run those apps). I think that I should be fine. If they would help, I can repost my cleaned-up MDP files. I can post graphs of potential, pressure, temperature, density, etc., from any phase in my protocol. Or you could just take my word for it that all of these parameters converge nicely during my equilibration procedure, and then remain stable throughout the production MD run. My target temperature is 310 K (37 C), and I get very close to that value on average. My average pressure and density readings are both a bit lower than my targets (0.80 bar and 988 kg/m^3, respectively), but they are consistent. I have examined a series of snapshots of my protein. It isn't undergoing any radical movements. My systems are on the small side, under 50,000 atoms. It's all amino acids and water molecules. Puzzled once again. Thanks for your advice! -- View this message in context: http://gromacs.5086.n6.nabble.com/Segmentation-fault-mdrun-mpi-tp5001601.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