Hello Stephan,
Does that mean we cannot append the data to the existing files in a normal
simulation
after a failure of the complete run
? If that is the case, should
I edit the number of steps in I my
'
.mdin
'
file also?
> Message: 3
> Date: Sun, 20 May 2018 17:27:10 +0200
> From:
>
> Stephan Schott <schottve.hhu.de>
> Subject: Re: [AMBER] Restart From Check point File
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAOBY5rjtbjwYZb69JD8m+=eF8JZJYuBgpDNN-f5yOC1dOiP5LA.mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi Midhun,
> The -A flag is for appending outputs, and as stated in the manual, mainly
> for replica exchange runs, so this is not what you should look for. For
> restarting your simulation using the -c flag should be enough, as you wrote
> in the command line you have there ("... -c run-prev.rst ..."). If this is
> the exact line you used before, you should have a run.rst, which can be
> used to restart your run. Just rename your files appropiatelly, and be
> aware that the -O flag means that if you use the same filenames, the
> previous files will be overwritten.
>
> Cheers,
>
> 2018-05-20 14:47 GMT+02:00 Midhun K Madhu <midhunk16.iiserb.ac.in>:
>
> > Hello all,
> >
> > While Running pmemd.cuda.MPI I am not able to use -A option which is, as
> > per AMBER16 manual, is the option for appending to the existing output
> > files. It says:
> >
> > -- unknown flag:
> > -A
> >
> >
> > usage: pmemd [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
> > [-ref refc -x mdcrd -v mdvel -frc mdfrc -e mden -inf mdinfo
> > -l logfile]
> > [-ng numgroups -groupfile groupfile -rem remd_method]
> > [-amd amdlog_name -gamd gamdlog_name -scaledMD
> > scaledMDlog_name -suffix output_files_suffix]
> >
> > ?I want to restart the run from the last .rst file generated?.
> >
> > To be more specific, I would like to know how to change my command from:
> >
> > pmemd.cuda.MPI -O -i run.mdin -p run.parm7 -c run-prev.rst -r run.rst -o
> > run.out -x run.nc
> >
> > to a command which restart my simulation? what changes should I do on
> > run.mdin, run-prev.rst and run.rst so that I can resume run.out and
> run.nc
> > ?
> >
> > *MIDHUN K MADHU*
> > Ph.D Student
> > Dept. of Biological Sciences
> > IISER Bhopal
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Received on Mon May 21 2018 - 22:30:02 PDT
