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.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> wrote: > >> >> >> 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 | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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