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

[Justin A. Lemkul]

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?
> 

Depending on the frequency with which you write to the .trr and .edr (nstxout, 
nstvout, nstenergy) there may be nothing in those files except the initial 
frame.  Use gmxcheck to confirm this.

-Justin

> 
> With Thanks,
> Vivek
> 
> 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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