[gmx-users] New files after simulation run

[Syed Azeem]

> Hi All,
>
> I have run an extended simulation for 90ns like this: (my previous run was
> for 10ns)
>
> grompp -f new.mdp -c old.tpr -o new.tpr
> mdrun -s new.tpr -cpi old.cpt
>
> I output mdrun STDOUT to an output file and it looks like this:
>
> ##############################################
>
> Back Off! I just backed up traj.trr to ./#traj.trr.2#
>
> Back Off! I just backed up traj_comp.xtc to ./#traj_comp.xtc.2#
>
> Back Off! I just backed up ener.edr to ./#ener.edr.2#
> starting mdrun 'Protein in water'
> 90000000 steps,  90000.0 ps (continuing from step 10000000,  10000.0 ps).
>
> NOTE: Turning on dynamic load balancing
>
>
> Writing final coordinates.
>
>  Average load imbalance: 2.3 %
>  Part of the total run time spent waiting due to load imbalance: 0.8 %
>  Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0
> % Y 0 %
>  Average PME mesh/force load: 0.716
>  Part of the total run time spent waiting due to PP/PME imbalance: 3.3 %
>
>
>                Core t (s)   Wall t (s)        (%)
>        Time:  9377991.988   379495.043     2471.2
>                          4d09h24:55
>                  (ns/day)    (hour/ns)
> Performance:       18.214        1.318
>
> ##########################################################
>
> I was expecting the new files to be generated with names "new.xtc"..
> "new.edr" ...etc, but I see in the output file the files generated are :
> (Moreover, there is no "new.log" file after the run finished)

You didn't pass the 'default filename' flag (-deffnm) in the mdrun command.

>
> traj_comp.xtc, traj.trr and ener.edr.
>
> Can someone please tell me why this happened or if something wrong has
> happened during the run?
>
> Thanks,
> DK