[gmx-users] Continuing a crashed run when running simulation in parts

[Erik Lindahl]

Hi,

In Gromacs 3.3 and earlier that depended on whether you were writing  
velocities & coordinates to the full precision trajectory - we can  
only restart from a frame where we have that.

Starting with Gromacs 4, runs are automatically checkpointed every 15  
minutes (by default). Then you can not only restart, but even append  
to the output trajectories.

Cheers,

Erik

On Oct 10, 2008, at 7:46 AM, vivek sharma wrote:

> Hi There,
> I am running a long MDS for one protein molecule in water, To avoid  
> error I am running the simulation in parts like 20 nsec each.
> Each time I am creating a new tpr, trr and edr using the tpbconv and  
> mdrun.
> Last time when I fired a job for 60-80 nsec then the job crashed  
> because of some power supply problem. Now I want to continue the job  
> from where it crashed ..
> while using ..... tpbconv with tpr, trr and edr file it gave me  
> message like
> _---------------------------------------
> trn version: GMX_trn_file (double precision)
> Read frame      4: step      0 time 60000.000
>
> Using frame of step 0 time 60000
> Opened emprmd_np24.edr as double precision energy file
> Reading frame      0 time 60000.000
>
> READ 3 PRESSURE COUPLING MU'S FROM emprmd_np24.edr
>
> 40000000 steps (80000 ps) remaining from first run.
> Writing statusfile with starting step          0 and length    
> 40000000 steps...
>                                  time      0.000 and length   
> 80000.000 ps
> -------------------------------------------------------------
>
> above message indicates that it is going to start the run from step  
> 0, which seems waste for me....
> Can I continue the job from where it crashed, or is it better to run  
> the 60-80 nsec job again?
>
>
> With Thanks,
> Vivek
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