[gmx-users] Restart

[Shrinath Kumar]

Hi,

You can find the file names that it looks for by doing gmx dump -cp
state.cpt.

On 31 July 2018 at 18:55, Eric Smoll <ericsmoll at gmail.com> wrote:

> Hi Mark,
>
> 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?
>
> Thanks again,
> Eric
>
> On Tue, Jul 31, 2018 at 11:33 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > 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.
> >
> > Mark
> >
> >
> > 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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