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

[Own 12121325]

and without append flag it will produce an output in the separate file,
won't it?

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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>