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.. 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 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>
<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>