[gmx-users] how to modify the md. log

[Justin A. Lemkul]

lina wrote:
> Hi,
> 
> My job terminated due to the storage out of the quote given by 
> administrator,
> 
> here the md.log is unusual, so when I resume the job, the results won't 
> append on it. but still running...
> 
> Here is the tail of md.log,
> 
>     DD  step 31424999 <tel:31424999> load imb.: force 20.8%  pme 
> mesh/force 1.936
> 
>            Step           Time         Lambda
>        31425000 <tel:31425000>    62850.00000        0.00000
> 
> <...snip...>
> 
> DD  step 31425999 <tel:31425999> load imb.: force 23.7%  pme mesh/force 
> 1.923
> 
>            Step           Time         Lambda
>        31426000 <tel:31426000>    62852.00000        0.00000
> 
> <...snip...>
>     Kinetic En.   Total Energy    Temperature [lina at hostname
> 
> 
> You may notice that the [lina at hostname] did not start in a new line.
> 
> there is md_step31441735.cpt
> and md_prev.cpt
> 
> what is the final step stored in the md_prev.cpt? How do I check ?
> 

It should be the step -cpt minutes before the later checkpoint was written.  Use 
gmxcheck to verify its contents.

> are there some chance to resume?
> 

Make sure the existing job has been killed (which sounds like it may or may not 
be the case) and simply restart from the appropriate checkpoint.

http://www.gromacs.org/Documentation/How-tos/Doing_Restarts

-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

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