[gmx-users] Segmentation fault while running MD simulation

[rainy908 at yahoo.com]

Hi Amit,

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.

Bests,
Lily

2009/11/13 Amit Choubey <kgp.amit at gmail.com>

> hi,
>
> 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
> trajectories.
>
> amit
>
>
>
> On Fri, Nov 13, 2009 at 3:53 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> rainy908 at yahoo.com wrote:
>>
>>> Hi,
>>>
>>> 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
>> tpbconv.
>>
>> -Justin
>>
>>
>>
>> --
>> ========================================
>>
>> 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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