[gmx-users] query about resuming a crashed mdrun

[abhisek Mondal]

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*
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*