rainy...@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.a...@gmail.com <mailto:kgp.a...@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 <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
rainy...@yahoo.com <mailto:rainy...@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
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