[gmx-users] Still having issues analyzing normal-mode hessian

Bryan Roessler roessler at uab.edu
Mon May 6 20:16:27 CEST 2013


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.


*Bryan Roessler | Graduate Research Assistant*
UAB | The University of Alabama at Birmingham
Knowledge that will change your world

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