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

[Justin Lemkul]

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

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