[gmx-users] query about resuming a crashed mdrun

[Mark Abraham]

Hi,

You'll need to manually append the files using trjcat and eneconv.

Mark

On Thu, 13 Apr 2017 11:56 abhisek Mondal <abhisek.mndl at gmail.com> wrote:

> Despite the naming problem will the traj.trr file contain the whole
> trajectory information ? The log file says:
> Gromacs binary or parallel settings not identical to previous run.
> Continuation is exact, but is not guaranteed to be binary identical.
>
> Probably because I used different number of processors for the same run's
> continuation. Will my final trajectory file contain all the steps ? If not
> then is there any way to join the trajectory information ?
>
> On Thu, Apr 13, 2017 at 2:32 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > Your second command didn't use deffnm flag, so mdrun interpreted your
> > intent as wanting most of the files to be named as the default. The 2016
> > release series refuses to run your second command precisely because of
> the
> > ambiguity about whether you intend to append, change names, etc.
> >
> > Mark
> >
> > On Thu, 13 Apr 2017 08:35 abhisek Mondal <abhisek.mndl at gmail.com> wrote:
> >
> > > Hi,
> > >     I was running mpirun -np 1600 mdrun_mpi  -deffnm npt on a protein
> and
> > > outputs were normal but the job crashed as not finished within given
> cpu
> > > time.
> > >
> > > Then I used mpirun -np 2048 mdrun_mpi -s npt.tpr -cpi npt.cpt to resume
> > the
> > > run from previous checkpoint. But, a whole lot of new files are being
> > > created. I thought it would be appended in the previous files.
> > >
> > > Previous files: npt.trr, npt.edr, npt.log, npt.cpt, npt_prev.cpt
> > > Files generated after
> > > resuming: state.cpt, state_prev.cpt, traj.trr, md.log, ener.edr
> > >
> > > If I watch the md.log file, it shows DD step as if it has resumed from
> > the
> > > last run. Did I made any mistakes there ? Am I going to get the whole
> > > trajectory information in parts ?
> > >
> > > I'm using gromacs-4.6.2
> > >
> > > Some suggestions will be highly appreciated.
> > >
> > > Thank you.
> > >
> > > --
> > > Abhisek Mondal
> > >
> > > *Senior Research Fellow*
> > >
> > > *Structural Biology and Bioinformatics Division*
> > > *CSIR-Indian Institute of Chemical Biology*
> > >
> > > *Kolkata 700032*
> > >
> > > *INDIA*
> > > --
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>
> --
> Abhisek Mondal
>
> *Senior Research Fellow*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
> --
> Gromacs Users mailing list
>
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