[gmx-users] Continue simulation

Jack Shultz js at drugdiscoveryathome.com
Wed Nov 25 01:03:34 CET 2009

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"?


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

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?



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