On 12/04/2012 3:30 PM, priya thiyagarajan wrote:
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..
At this point, you should have looked at your .log file and your stdout
and stderr files to see why the simulation stopped, rather than blindly
continuing.
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
2.24598e-05
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 <http://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
There should be more descriptive error output somewhere. In any case,
you are probably
http://www.gromacs.org/Documentation/Terminology/Blowing_Up and need to
follow the diagnostic advice there.
Mark
<http://www.gromacs.org/Documentation/Terminology/Blowing_Up>
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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