[gmx-users] Restart a simulation from a power source failure

[Justin A. Lemkul]

Luís Pereira wrote:
> Hi Justin,
> 
> Thank you for your quick answer.
> All the files are in the working directory but have different names, 
> e.g., the .trr is not traj.trr but 7fboh3.trr, and so on.

If you do not supply filenames, then the defaults are assumed.  This is true of 
all Gromacs programs.

> I've backed up the working directory, run gromacs with all output file 
> names written in command line and now everything is working fine:
> 
>     1000000 steps,   1000.0 ps (continuing from step 878000,    878.0 ps).
> 
>  
> Well, i'll have to wait to see if the final results are ok.
> 

They should be, provided the command issued is correct.

-Justin

> Luís
> 
> 
> 
> On 8 August 2011 21:47, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Luís Pereira wrote:
> 
>         Hi all,
> 
>         I'm trying to restart a simulation from a power source failure,
>         but mdrun complains about a missing .trr file:
> 
>            Program mdrun, VERSION 4.0.7
>            Source code file: ../../../../src/gmxlib/gmxfio.__c, line: 737
> 
>            Can not open file:
>            traj.trr
> 
> 
>         The manual says that there is no need to supply more information
>         than:
> 
>            mdrun -s topol.tpr -cpi state.cpt -append
> 
> 
>         Do I have to write all the output files in the above command
>         line? Or there was something wrong when gromacs wrote the
>         checkpoint file?
> 
> 
>     If you're appending, then all the expected files must be present in
>     the working directory, unmodified.  It appears that this is not the
>     case, as traj.trr is missing.  You can always use -noappend and
>     concatenate any relevant output later.
> 
>     -Justin
> 
>     -- 
>     ==============================__==========
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
>     ==============================__==========
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================