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

[lina]

On Sat, Sep 10, 2011 at 8:45 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

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

Thanks.


>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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-- 
Best Regards,

lina
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