[gmx-users] Segmentation fault while running MD simulation

[rainy908 at yahoo.com]

Hi all,

I've encountered a problem while trying to run Gromacs on my coarse-grained
molecule.  I've already performed the initial energy minimization.  I tried
to run the inital MD simulation, but the job was cut short due to a
segmentation fault, as mentioned in the output file:

^Mstep 0^Mstep 100, will finish Wed Dec 16 16:55:17 2009^Mstep 200, will
finish Wed Dec 16 07:04:11 2009^Mstep 300, will finish Wed Dec 16 12:59:33
2009^Mstep 400, will finish Wed Dec 16 09:02:03 2009^Mstep 500, will finish
Wed Dec 16 12:12:01 2009^Mstep 600, will finish Wed Dec 16 14:18:47
2009^Mstep 700, will finish Wed Dec 16 15:49:22 2009^Mstep 800, will finish
Wed Dec 16 13:29:16 2009^Mstep 900, will finish Wed Dec 16 14:45:15
2009^Mstep 1000, will finish Wed Dec 16 15:46:03 2009

/opt/gridengine/default/spool/
compute-0-7/job_scripts/182710: line 28: 18851 Segmentation fault      (core
dumped) $MDRUN -v -nice 0 -np $NSLOTS -s npg3_4.tpr -o npg3_4.trr -c
confout.gro -g npg3_4.log -x npg3_4.xtc -e npg3_4.edr
/opt/gridengine/default/spool/compute-0-7/job_scripts/182710: line 31: -s:
command not found

Does anyone know what could be causing the problem?  Should it be of
interest, my em.mdp is included at the bottom.

Thanks for your help!

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
em.mdp
; VARIOUS PREPROCESSING OPTIONS =
title                    =
cpp                      = /lib/cpp
include                  =
define                   =

; RUN CONTROL PARAMETERS =
integrator               = steep
; start time and timestep in ps =
tinit                    = 0
dt                       = 0.02
nsteps                   = 1000

; ENERGY MINIMIZATION OPTIONS =
;emtol                    = 0.00001
;emstep                   = 0.1
;nstcgsteep               = 1000

emtol                    = 10
emstep                   = 0.01
nstcgsteep               = 1000

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

md.mdp

; RUN CONTROL PARAMETERS =
; MARTINI - Most simulations are stable with dt=40 fs,
; some (especially rings) require 20-30 fs.
; The range of time steps used for parametrization
; is 20-40 fs, using smaller time steps is therefore not recommended.

integrator               = md
; start time and timestep in ps
tinit                    = 0
dt                       = 0.020
;nsteps                   = 10000 ; initial step
nsteps                           = 10000000 ; 200 ns @ dt=0.02

; number of steps for center of mass motion removal =
nstcomm                  = 1
comm-grps                =
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