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On 12/04/2012 3:30 PM, priya thiyagarajan wrote:
<blockquote
cite="mid:CAEuVTxCdvQh8FK=6udtNc+kMqz4VVYqrH6pK8bq68KFBzmYCpg@mail.gmail.com"
type="cite">hello sir, <br>
<br>
Thanks for your kind reply..<br>
<br>
i am performing final md run for 60molecules ..<br>
<br>
after i submitted my job for 5ns, when i analyse the result my run
is completed only for 314ps initially..</blockquote>
<br>
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.<br>
<br>
<blockquote
cite="mid:CAEuVTxCdvQh8FK=6udtNc+kMqz4VVYqrH6pK8bq68KFBzmYCpg@mail.gmail.com"
type="cite"> 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..<br>
<br>
when i analysed my log file it just showing like this<br>
<br>
<br>
DD step 268999 load imb.: force 1.5%<br>
<br>
Step Time Lambda<br>
269000 538.00000 0.00000<br>
<br>
Energies (kJ/mol)<br>
G96Angle Proper Dih. Improper Dih. LJ-14
Coulomb-14<br>
9.84673e+03 5.10424e+03 1.80376e+03 2.90591e+03
-2.97052e+03<br>
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
Potential<br>
9.69125e+04 -1.59583e+03 -7.80231e+05 -3.04364e+04
-6.98661e+05<br>
Kinetic En. Total Energy Temperature Pres. DC (bar)
Pressure (bar)<br>
1.17775e+05 -5.80886e+05 2.97568e+02 -1.04033e+02
2.31825e+01<br>
Constr. rmsd<br>
2.24598e-05<br>
<br>
<br>
<br>
when i checked my errorfile i got this is because of segmentation
fault..<br>
<br>
my errorfile showed like this<br>
<br>
Wrote pdb files with previous and current coordinates<br>
Wrote pdb files with previous and current coordinates<br>
/var/spool/PBS/mom_priv/jobs/<a moz-do-not-send="true"
href="http://244266.vega.SC">244266.vega.SC</a>: 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<br>
</blockquote>
<br>
There should be more descriptive error output somewhere. In any
case, you are probably <a
href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up">http://www.gromacs.org/Documentation/Terminology/Blowing_Up</a>
and need to follow the diagnostic advice there.<br>
<br>
Mark<br>
<br>
<a
href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up"></a>
<blockquote
cite="mid:CAEuVTxCdvQh8FK=6udtNc+kMqz4VVYqrH6pK8bq68KFBzmYCpg@mail.gmail.com"
type="cite">
<br>
<br>
i searched in archieves but i didnt get the point clearly... <br>
<br>
can anyone please help me by explaining that reason for my problem
and solve it.<br>
<br>
i am waiting for your reply..<br>
<br>
pls help me with your valuable answer..<br>
<br>
i am using gromacs 4.5.5 version.<br>
<br>
thanking you,<br>
<br>
<br>
<br>
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<br>
</blockquote>
<br>
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