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

Justin Lemkul jalemkul at vt.edu
Thu Jun 21 01:12:27 CEST 2018

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


> 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 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


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