[gmx-users] NMA and g_nmeig segmentation fault

Michael Howard howard.michaelp at gmail.com
Mon Aug 6 23:07:28 CEST 2012

Hello All -- I'm trying to do a normal modes analysis of a fairly
large crystal system (~20,000 atoms) in double-precision GROMACS. The
system is xy periodic with 2 9-3 walls, and has periodic molecules. I
first minimized the structure with L-BFGS to 1e-5 tolerance with
switched vdW interactions and PME electrostatics (3dc geometry).

When I tried to run g_nmeig on the matrix, I received the following
error message from the shell

/var/spool/pbs/mom_priv/jobs/2480011.lionxj.rcc.psu.edu.SC: line 7:
3205 Segmentation fault      g_nmeig_d -f wall3_nm -s wall3_nm -T 300
-first 1 -last 20000 -of wall3_efreq -ol wall3_eigval -v wall3_eigvec

The last thing written to the g_nmeig output is
Reading file wall3_nm.tpr, VERSION 4.5.5 (double precision)
Reading file wall3_nm.tpr, VERSION 4.5.5 (double precision)
Reading double precision matrix generated by Gromacs VERSION 4.5.5

I was able to successfully run NMA using the same code on a similar
system that was only 1/3 of the current size (reaction-field-zero
electrostatics) and also on a system 1/3 of the size with xyz
periodicity and PME electrostatics, and received no segmentation fault
error. I'm a little bit baffled about the source of the segmentation
error, because I would have expected it to crash during the Hessian
calculation if there were a problem with allocating system memory or
essentially singular forces. Has anyone else encountered a similar

Thanks in advance for your help.

-- Mike Howard

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