[gmx-users] interrupt of gmx mdrun

Andrew Bostick andrew.bostick1 at gmail.com
Sat Jun 29 12:15:40 CEST 2019

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

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

What is the reason of this interruption. How to resolve that?


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