[gmx-users] interrupt of gmx mdrun

[Dallas Warren]

Check the output file from the job scheduler i.e. slurm-jobnumber.slurm

That will contain the error output information that will indicate what
has gone wrong.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Sat, 29 Jun 2019 at 20:15, Andrew Bostick <andrew.bostick1 at gmail.com> wrote:
>
> 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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