[gmx-users] Continuation of the gromacs job using gmx convert-tpr

[Own 12121325]

In fact there is an alternative trick :-)
If I rename a tpr file via gmx convert-tpr  and then run mdrun using this
new tpr as well as previous checkpoint, it will produce all pieces of the
trajectory in the separate file:

gmx convert-tpr -s step7_1.tpr -o step7_2.tpr -extend 50000
mpirun -np ${NB_TASKS} mdrun -v -deffnm step7_2 -cpi step7_1.cpt

If I add -noappend flag to the mdrun, its also do the same job but also
will add suffix pat002 to each of the new file (that is not necessary for
me since I have already renamed tpr).

Gleb


2018-06-21 14:17 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 6/21/18 2:35 AM, Own 12121325 wrote:
>
>> and without append flag it will produce an output in the separate file,
>> won't it?
>>
>
> No, because appending is the default behavior. Specifying -append just
> invokes what mdrun does on its own. If you want a separate file, add
> -noappend to your mdrun command.
>
> -Justin
>
>
> gmx convert-tpr -s init.tpr -o next.tpr -extend 500000
>> gmx mdrun -s next.tpr -cpi the_last_chekpoint.cpt
>>
>> 2018-06-21 1:12 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:
>>
>>
>>> On 6/19/18 4:45 AM, Own 12121325 wrote:
>>>
>>> Hello Justin,
>>>>
>>>> could you specify please a bit more. Following your method, if the
>>>> simulation has been terminated by crash without producing gro file so to
>>>> re-initiate it I only need one command:
>>>>
>>>> gmx mdrun -s initial.tpr -cpi the_last_chekpoint.cpt -append
>>>>
>>>> where the last_checkpoint should be something like initial.cpt or
>>>> initial_prev.cpt
>>>>
>>>> Right.
>>>
>>> but In case if my simulation has been finished correctly e.g. for 50 ns
>>> and
>>>
>>>> I now need to extend it for another 50 ns,  should I do the following
>>>> trick
>>>> with 2 GMX programs:
>>>>
>>>> gmx convert-tpr -s init.tpr -o next.tpr -extend 500000
>>>> gmx mdrun -s next.tpr -cpi the_last_chekpoint.cpt -append
>>>>
>>>> it will produce the second part of the trajectory as the new file
>>>> (next.trr) or merge together the first and the second part ?
>>>>
>>>> You're specifying -append, so the output will be concatenated by mdrun.
>>> That's also been default behavior for as long as I can remember, too :)
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
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>>> http://www.thelemkullab.com
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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