[gmx-users] mdrun segmentation fault

priya thiyagarajan priya.thiyagarajan09 at gmail.com
Thu Apr 12 07:30:11 CEST 2012

hello sir,

Thanks for your kind reply..

i am performing final md run for 60molecules ..

after i submitted my job for 5ns, when i analyse the result my run is
completed only for 314ps initially.. then i extende my simulation.. but
again it completed only for 500ps.. initially i thought because of queue
limit its getting stopped.. but 3rd time i extended my simulation it came
for 538ps..

when i analysed my log file it just showing like this

DD  step 268999 load imb.: force  1.5%

           Step           Time         Lambda
         269000      538.00000        0.00000

   Energies (kJ/mol)
       G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
    9.84673e+03    5.10424e+03    1.80376e+03    2.90591e+03   -2.97052e+03
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
    9.69125e+04   -1.59583e+03   -7.80231e+05   -3.04364e+04   -6.98661e+05
    Kinetic En.   Total Energy    Temperature Pres. DC (bar) Pressure (bar)
    1.17775e+05   -5.80886e+05    2.97568e+02   -1.04033e+02    2.31825e+01
   Constr. rmsd

when i checked my errorfile i got this is because of segmentation fault..

my errorfile showed like this

Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
/var/spool/PBS/mom_priv/jobs/244266.vega.SC: line 11: 26308 Segmentation
fault      mdrun -s md.tpr -o md3.trr -c md3.pdb -e md3.edr -g md3.log -cpi
state2.cpt -cpo state3.cpt -x traj3.xtc -noappend

i searched in archieves but i didnt get the point clearly...

can anyone please help me by explaining that reason for my problem and
solve it.

i am waiting for your reply..

pls help me with your valuable answer..

i am using gromacs 4.5.5 version.

thanking you,
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