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

[Own 12121325]

P.S. what the difference between name.cpt and name_prev.cpt produced by
mdrun? What check-point should correspond to the last snapshot in trr file ?

2018-06-22 10:17 GMT+02:00 Own 12121325 <own12121325 at gmail.com>:

> 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
>>>>
>>>> jalemkul at vt.edu | (540) 231-3129
>>>> 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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>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
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>
>