Version 4 and Newer

A simulation that has terminated, but not completed (e.g. because of queue limits,  power failure or the use of the -maxh option of mdrun) can be continued without needing to use tpbconv (which is now called gmx convert-tpr as of version 5.0). You may or may not wish to use -append in your mdrun command in this case. Otherwise, a simulation that has completed can be extended using tpbconv, mdrun and checkpoint files (.cpt). First, the number of steps or time has to be changed in the .tpr file, then the simulation is continued from the last checkpoint with mdrun. This will produce a simulation that will be the "same" as if a continuous run was made (but see reproducibility for more discussion).

tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt

You might want to use the -append option of mdrun to append the new output to the old files. Note that this will only work when the old output files have not been modified by the user.  Appending is the default behavior as of version 4.5.

If you would like to change the default filenames while running a lengthy simulation in manageable parts, then cyclically running commands such as the following will work: (with suitable values for name and time)

mdrun -deffnm ${name} -cpi ${name} -append
tpbconv -s ${name} -o ${name}_new.tpr -extend ${time}
mv ${name}_new.tpr ${name}.tpr

When running in a queuing system, it is useful to set the number of steps you want for the total simulation with grompp or tpbconv and use the -maxh option of mdrun to gracefully stop the simulation before the queue time ends. With this procedure you can simply continue by letting mdrun read checkpoint files and no other tools are required. However, if your queueing system permits job suspension, the -maxh mechanism will be unaware of the time spent suspended, and you may simulate for less wall time than you would expect.

The time can also be extended using the -until and -nsteps options with tpbconv.

A simulation can be continued without the checkpoint file, which will be non-binary identical and will have small errors that, for most situations, are negligible. The reason for the errors is that the trajectory and energy files do not store all the state variables of the thermostats and barostats.  If this is the case, you must make use of the version 3.3.3 procedure below.

grompp -f new.mdp -c old.tpr -o new.tpr -t old.cpt
mdrun -s new.tpr

grompp -f new.mdp -c old.tpr -o new.tpr
mdrun -s new.tpr -cpi old.cpt