[gmx-users] Segmentation fault while running MD simulation

[Justin A. Lemkul]

rainy908 at yahoo.com wrote:
> 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.
> 

2 steps?  Your original post with verbose output indicated at least 1000 steps 
had completed, certainly enough to see what's going on in the trajectory.

> Could the size of my system caused it to crash?  Also, in my md.log 
> file, the only error that I see is:
> 

There is no connection I can see between system size and crashing.  There was a 
bug in version 4.0 that Berk fixed prior to the release of version 4.0.2, but I 
think I was the only one who ever saw it, for some reason that is beyond me :) 
What version of Gromacs are you using?

> 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)
> 

I thought constraints were set to "none" in your system; I doubt this will make 
much of a difference, but the MARTINI developers suggest this setting as well.

> 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.
> 

I see nothing unreasonable about the EM results.  Definitely watch the 
trajectory to get any clues as to where the instability starts.  If you can 
afford the disk space, set nstxtcout = (some very small value) to try to capture 
as many frames as possible before the crash.

Did grompp report any warnings about your settings?  What does the tc-grp 
SOLVENT contain?  Is it just solvent + ions?

-Justin

> Bests,
> Lily
> 
> 2009/11/13 Amit Choubey <kgp.amit at gmail.com <mailto: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
>     <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>         rainy908 at yahoo.com <mailto: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 <http://vt.edu> | (540) 231-9080
>         http://www.bevanlab.biochem.vt.edu/Pages/Personal/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

========================================