[gmx-users] Segmentation fault while running MD simulation

[Justin A. Lemkul]

rainy908 at yahoo.com wrote:
> 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                =
> 

Is this the entirety of your md.mdp file?  If so, all other options will be set 
to default, and these may or may not (read: likely will not) be appropriate for 
your system.  A number of factors can lead to a segmentation fault, but in 
generic terms, something became unstable.  Check the output - look at the 
trajectory to see where things start to fall apart.  Helpful messages are 
usually printed in the log file as well.  Beyond that, please consult the following:

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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