[gmx-users] Restart

Mark Abraham mark.j.abraham at gmail.com
Tue Jul 31 19:33:43 CEST 2018


As you can probably see in the log file, mdrun is refusing to do the
default restart with appending from the checkpoint because the output
filenames when you wrote the files are different to the ones supplied by
the mdrun defaults now. I'm sure the behavior of mdrun has been improved
since then, but in choosing to rename all the files you have created for
yourself the problem of making sure the restart also has all the names
matching. Perhaps -noappend will let you get something done, but I strongly
suggest using directories for your project organization using the default
file names, rather than manually managing file names.


On Tue, Jul 31, 2018, 04:14 Eric Smoll <ericsmoll at gmail.com> wrote:

> Hello GROMACS users,
> I had a simulation terminate unexpectedly very close to completion and I
> would like to resume the simulation from a checkpoint file.
> my mdrun flags are -cpi, -s, -o, -x, -c, -e, -g, and -cpo.
> All of the associated files are present (except the -c file since there was
> a crash).  Looking at the last saved checkpoint in the log file and running
> "gmx check -f state.cpt" on the cpo file "state.cpt" confirms that the
> proper time has been saved.  An important point is that the files names I
> provided are not used because gromacs has added the infix ".part0001"
> The GROMACS 2016 page on "Managing Long Simulations" claims I can restart
> with the command "gmx mdrun -cpi state.cpt."  However, this starts the
> simulation at step 0 and does not append to the current file (instead
> adding to a file without the ".part0001" infix).  It is unclear if this
> will only execute the remaining number of steps or not.
> How can I get mdrun to launch this restart correctly?
> Best,
> Eric
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