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

[Justin Lemkul]

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

-- 
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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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