Dear all, I have some membrane protein systems running in our cluster using gmx4.0.4. The minimizations finish with reasonable potential energy values (of the order of 10^-5 with maximum forces of the order of 10^-3). Then I am trying to run several 1-ns-long equilibration MD trajectories with progressive relaxation of the protein positional restraints decreasing the force constant from 1000 kJ/mol/nm^2 to 0, all using PME on 16 processors. The PME load is about 25% in all cases. Some systems run with no problem but others abort with final lines in the mdrun.log file like these: MPI Application rank 4 killed before MPI_Finalize() with signal 11 MPI Application rank 15 killed before MPI_Finalize() with signal 11
It is worth to mention that some of the simulations that present this segmentation fault are just extensions of trajectories that finished successfully, with the only change of reducing the force constant in 200 KJ/mol/nm^2, for example from 800 to 600 or from 1000 to 800. Other simulations present this problem just during the first equilibration step with a force constant of 1000. IMPORTANT: A copy of the same topol.tpr files run on my local computer (on one processor) with no problem, so I do believe that it is not a problem of the initial configuration. Anyone knows the source of this problem? Thanks a lot for any help... Angel. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
