[gmx-users] Segmentation fault while running MD simulation
rainy908 at yahoo.com
rainy908 at yahoo.com
Sat Nov 14 03:02:13 CET 2009
My system is quite large, comprising of a molecule, water, and Na+ ions,
summing up to 233863 (!) entities total. Regarding the segmentation fault,
the MD simulation only ran for 2 steps before the system crashed.
Could the size of my system caused it to crash? Also, in my md.log file,
the only error that I see is:
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
Steepest Descents converged to machine precision in 36 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -6.9601880e+06
Maximum force = 4.1059329e+02 on atom 454
Norm of force = 2.6538130e+03
While I have encountered these messages before with other systems in the
past, I did not encounter any major problems (i.e. segmentation faults)
during their MD simulations.
2009/11/13 Amit Choubey <kgp.amit at gmail.com>
> could you specify the system size?
> How many steps did it run before you got the segmentation fault? Try to
> find if everything went ok until the segmentation fault by saving log and
> On Fri, Nov 13, 2009 at 3:53 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>> rainy908 at yahoo.com wrote:
>>> The relevant lines of my script are the following:
>>> line 27: # Run MD and write output to /nas2 disk
>>> line 28: $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
>>> line 29:
>>> line 30: # MDRUN completes: now make the next run file for a further 200
>>> ps, to be run by next job
>>> line 31: $TPBCONV -s npg3_4.tpr -f npg3_4.trr -e npg3_4.edr -o
>>> npg3_4_2.tpr -extend 200000
>>> Since line 31 would be carried out after line 28, I'm not sure why the
>>> comment "-s: command not found" is relevant?
>> Because mdrun is exiting, so the script is moving on. Perhaps the system
>> isn't recognizing the $TPBCONV environment variable, and thus is
>> interpreting "-s" as a separately command rather than an option passed to
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
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