Hello, I have successfully generated a 945MB mtx hessian storing the normal modes of a ~1500AA protein using mdrun with the "nm" integrator and no cutoffs. However, when I try to analyze the normal modes and create trajectories using g_nmeig, I can't seem to generate any output. I am running g_nmeig_mpi_d with the following options: "mpiexec_mpt g_nmeig_mpi_d -f input.mtx -s NMA.tpr -of NMA_freq.xvg -ol NMA_val.xvg -v NMA_vec.trr" and have been letting it run a few times for up to 5 days on 128 Itanium nodes with 120gb maximum memory. When the job finally aborts after running out of cpu time, I get a standard output file that's about 8GB (which I am unable to open). Is there a way to force g_nmeig to generate some output or at least show me what is going on? Am I running it with the correct options? There isn't a lot of documentation on these normal-mode specific programs so I don't know how to begin troubleshooting.
Thanks, *Bryan Roessler | Graduate Research Assistant* UAB | The University of Alabama at Birmingham *uab.edu/cmdb* Knowledge that will change your world -- 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
