ericsmoll at gmail.com
Tue Jul 31 19:55:52 CEST 2018
Thanks for the reply. I do use directories for project management but, up
until now, I also had a preference for custom filenames. Lesson learned.
I need to use the default naming scheme if I want smooth restarts. I
wrongfully assumed that the consistent use of output filename flags in
GROMACS tools meant that custom output filenames were supported and
encouraged. I wrongfully assumed that GROMACS code snippets that suppress
custom output filenames were just being concise for clarity and simplicity.
When attempting to restart, it would be nice if mdrun listed the file names
it is looking for. Can I find this information anywhere or is it
completely hidden from the user?
On Tue, Jul 31, 2018 at 11:33 AM, Mark Abraham <mark.j.abraham at gmail.com>
> 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
> > a crash). Looking at the last saved checkpoint in the log file and
> > "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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