[gmx-users] New files after simulation run

[RAHUL SURESH]

On Mon, Sep 25, 2017 at 3:13 PM, Deep kumar <deepak.choubey86 at gmail.com>
wrote:

> 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
>

I am not very sure about this step..

But instead you can use the following commands



*gmx convert-tpr -s md.tpr -extend 250000 -o extend2.tpr  gmx mdrun -v
-deffnm extend2*


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)
>
> 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
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*