[gmx-users] Resuming of calculation from last *.cpt

[James Starlight]

In that case I've obtain error

Fatal error:
Failed to lock: md_init.log. Already running simulation?

What does it means ? the md_init.log is present in the wor dir

2012/9/15 Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 9/15/12 10:11 AM, James Starlight wrote:
>>
>> Jusin,
>>
>> yes, the initial files were named as the md_initial
>>
>> the simulation was resumed correctly but all output data was saved
>> into new set of files with the default names. In my case I want that
>> the resummed simulation data will write to the existing (md_initial)
>> files without creation of new trajectory and other files.
>>
>
> mdrun -cpi -append -deffnm md_initial
>
> Should do the trick.
>
> -Justin
>
>
>> James
>>
>> 2012/9/15 Justin Lemkul <jalemkul at vt.edu>:
>>>
>>>
>>>
>>> On 9/15/12 10:03 AM, James Starlight wrote:
>>>>
>>>>
>>>> Justin,
>>>>
>>>> In accordance to the manual I've re-launched my simulation by the
>>>> command
>>>> mpiexec -np 48 mdrun_mpi.openmpi -v -s md_initial  -cpi md_initial
>>>> -append
>>>>
>>>>
>>>> where md_initial is the name of the files from the run which I want to
>>>> continue.
>>>>
>>>> As the result this produce new files with the default names traj.trr
>>>> ener.edr etc. In those files the trajectory have been calculated from
>>>> the last frame of the md_initial.cpt file. So as the result I've
>>>> obtain again 2 set of output files ( from old and new runs). IS it
>>>> possible to continue the calculations and save output within the
>>>> existing files (md_initial) without creation of new ones ?
>>>>
>>>
>>> The names of the files produced depend on what is stored in the .cpt
>>> file.
>>> mdrun will only append to files with those names.  I don't have a clear
>>> picture of what you've done so it's impossible to say whether or not this
>>> is
>>> the expected outcome, but the checkpointing feature is very robust so I
>>> suspect it is.  Were all of  your file names originally called
>>> md_initial?
>>> If you've re-named them, the appending will fail for that very reason.
>>>
>>>
>>> -Justin
>>>
>>> --
>>> ========================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> 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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>
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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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