Hi gromacs users,
I am doing MD simulation of a protein (from pdb ). After equilibration
phases, I used following commands:
gmx_mpi grompp -f md.mdp -c npt.gro -t npt.cpt p topol.top -o md.tpr -n
index.ndx
gmx_mpi mdrun -v -nb gpu -deffnm md >& md.job &
But, mdrun was interrupted in step 8237500. I repeated last command. This
happened again but in step 6837500.
The last lines of md.log file is as follows:
Step Time Lambda
6837500 13675.00000 0.00000
Energies (kJ/mol)
Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
5.30550e+03 6.71343e+03 2.61548e+02 2.78159e+03 3.61962e+04
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
4.03766e+04 -3.33403e+03 -4.03105e+05 2.26409e+03 -3.12540e+05
Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar)
5.98029e+04 -2.52737e+05 2.95155e+02 -2.28999e+02 5.62166e+00
Constr. rmsd
2.50195e-05
What is the reason of this interruption. How to resolve that?
Best,
Andrew
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