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

[Justin Lemkul]

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

==================================================