[gmx-users] Continue simulation

Justin A. Lemkul jalemkul at vt.edu
Wed Nov 25 01:20:43 CET 2009

Jack Shultz wrote:
> Is it ok just to use tpbconv, even though we get this message
> "Continuation should be done by loading a checkpoint file with mdrun -cpi"?

Please see the last paragraph in the "Version 4" section here:


> ++++++++++++++++++++++++++++++++++
> I have tried mdrun using the -cpi flag
> mdrun -v -x -c -o -e -cpo next.cpt -cpi md.cpt -deffnm md
> Then when I run the next using the next.cpt, it seems to do the next
> time interval because it is actually taking time to compute timesteps
> mdrun -v -x -c -o -e -cpo next2.cpt -cpi next.cpt -deffnm md
> using the checkpoint, i get less standard output telling me the
> tototal simulation time
> while preping the mdrun using  tpbconv -s md.tpr -f md.trr -e md.edr
> -time 2 -o next.tpr

This is the obsolete way to continue a simulation, i.e. version 3.3.3 and 
earlier.  Follow the instructions in the above link for version 4.


> I get this output.
> starting mdrun 'Protein in water'
> 1500 steps,      3.0 ps (continuing from step 500,      1.0 ps).
> step 500, will finish Wed Nov 25 00:15:43 2009
> step 700, remaining runtime:   258 s
> So should there be any difference in the results then?


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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