[gmx-users] tpbconv to extend a simulation

Justin A. Lemkul jalemkul at vt.edu
Tue Mar 6 17:09:15 CET 2012

Juliette N. wrote:
> Hello all,
> I read the online instruction on how to extend a run. I just wanted to
> double check the procedure because of the NOTE below after issuing
> tpbconv –f old.trr -s old.tpr -e old.edr -o old-extend.tpr -until 10000
> NOTE: Reading the state from trajectory is an obsolete feaure of tpbconv.
>       Continuation should be done by loading a checkpoint file with mdrun -cpi
>       This guarantees that all state variables are transferred.
>       tpbconv is now only useful for increasing nsteps,
>       but even that can often be avoided by using mdrun -maxh
> Modifying ir->bContinuation to TRUE
> NOTE: The simulation uses pressure coupling and/or stochastic dynamics.
> tpbconv can not provide binary identical continuation.
> If you want that, supply a checkpoint file to mdrun
> ------------------------------------------------------------------------------
> then used cpi option to include checkpoint file :
> mdrun -deffnm old-extend -s -o -c -g -e -x -cpi old.cpt
> Am I doing things correctly?

As implied by the note, the -f and -e flags and the files they provide are 
unnecessary.  The checkpoint file guarantees a correct continuation.  The exact 
commands you need (substituting -extend or -until, whichever you prefer, though 
-until is a bit more reliable where rounding is concerned) are here:




Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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