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 <jalem...@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
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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry
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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
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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