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

[Own 12121325]

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 ?

Thank you!

Gleb


2018-06-18 21:00 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 6/18/18 9:11 AM, Own 12121325 wrote:
>
>> thanks Justin for the suggestions!
>>
>> but generally this antiquated approach produces correct thermodynamical
>> ensembles (since I do not call grompp again), doesn't it?  Following this
>> method the last snapshot from the trajectory will be taken to continue
>> job,
>> right ?
>>
>
> Possibly. I haven't done this since the 3.3.x series, though, because
> checkpoints guarantee an exact continuation. The combination of .trr + .edr
> is not exact but is close. It probably all comes out in the noise of the
> simulation, but if you can choose between an exact continuation and an
> approximate one, why not be exact? :)
>
> -Justin
>
>
> 2018-06-15 14:22 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:
>>
>>
>>> On 6/14/18 4:01 AM, Own 12121325 wrote:
>>>
>>> Hello,
>>>>
>>>> I wonder to know if it's necessary to provide edr file for the completed
>>>> part of the simulation in order to continue the md job assuming that I
>>>> provide the trajectory (with coordinates and velocities) using
>>>> gmx convert-tpr.
>>>>
>>>> Does the ensembles produced by mdrun will be the same following these
>>>> two
>>>> methods of the continuation:
>>>>
>>>> gmx convert-tpr -s prev.tpr -f prev.trr -o next.tpr -extend 1000
>>>> gmx mdrun -v -deffnm next
>>>>
>>>> compared to
>>>>
>>>> gmx convert-tpr -s prev.tpr -f prev.trr *-e prev.edr* -o next.tpr
>>>> -extend
>>>> 1000
>>>> gmx mdrun -v -deffnm next
>>>>
>>>> You don't use either .trr or .edr files. Just generate the new .tpr file
>>> with however much more time you want and pick up from the exact time
>>> point
>>> you were with mdrun -cpi prev.cpt. Use of .trr and .edr files to extend
>>> simulations is an antiquated approach.
>>>
>>> -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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